Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma.

Posterior fossa A (PFA) ependymomas are lethal malignancies of the hindbrain in infants and toddlers. Lacking highly recurrent somatic mutations, PFA ependymomas are proposed to be epigenetically driven tumors for which model systems are lacking. Here we demonstrate that PFA ependymomas are maintained under hypoxia, associated with restricted availability of specific metabolites to diminish histone methylation, and increase histone demethylation and acetylation at histone 3 lysine 27 (H3K27). PFA ependymomas initiate from a cell lineage in the first trimester of human development that resides in restricted oxygen. Unlike other ependymomas, transient exposure of PFA cells to ambient oxygen induces irreversible cellular toxicity. PFA tumors exhibit a low basal level of H3K27me3, and, paradoxically, inhibition of H3K27 methylation specifically disrupts PFA tumor growth. Targeting metabolism and/or the epigenome presents a unique opportunity for rational therapy for infants with PFA ependymoma.

Childhood cerebellar tumours mirror conserved fetal transcriptional programs.

Study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. Here we use single-cell transcriptomics to study more than 60,000 cells from the developing mouse cerebellum and show that different molecular subgroups of childhood cerebellar tumours mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. The Sonic Hedgehog medulloblastoma subgroup transcriptionally mirrors the granule cell hierarchy as expected, while group 3 medulloblastoma resembles Nestin+ stem cells, group 4 medulloblastoma resembles unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumours demonstrates that many bulk tumours contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumours as a disorder of early brain development and provide a proximate explanation for the peak incidence of cerebellar tumours in early childhood.

Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma.

In cancer, recurrent somatic single-nucleotide variants-which are rare in most paediatric cancers-are confined largely to protein-coding genes1-3. Here we report highly recurrent hotspot mutations (r.3A>G) of U1 spliceosomal small nuclear RNAs (snRNAs) in about 50% of Sonic hedgehog (SHH) medulloblastomas. These mutations were not present across other subgroups of medulloblastoma, and we identified these hotspot mutations in U1 snRNA in only <0.1% of 2,442 cancers, across 36 other tumour types. The mutations occur in 97% of adults (subtype SHHδ) and 25% of adolescents (subtype SHHα) with SHH medulloblastoma, but are largely absent from SHH medulloblastoma in infants. The U1 snRNA mutations occur in the 5' splice-site binding region, and snRNA-mutant tumours have significantly disrupted RNA splicing and an excess of 5' cryptic splicing events. Alternative splicing mediated by mutant U1 snRNA inactivates tumour-suppressor genes (PTCH1) and activates oncogenes (GLI2 and CCND2), and represents a target for therapy. These U1 snRNA mutations provide an example of highly recurrent and tissue-specific mutations of a non-protein-coding gene in cancer.

Lipidomic-Based Approach to 10 s Classification of Major Pediatric Brain Cancer Types with Picosecond Infrared Laser Mass Spectrometry.

Picosecond infrared laser mass spectrometry (PIRL-MS) is shown, through a retrospective patient tissue study, to differentiate medulloblastoma cancers from pilocytic astrocytoma and two molecular subtypes of ependymoma (PF-EPN-A, ST-EPN-RELA) using laser-extracted lipids profiled with PIRL-MS in 10 s of sampling and analysis time. The average sensitivity and specificity values for this classification, taking genomic profiling data as standard, were 96.41 and 99.54%, and this classification used many molecular features resolvable in 10 s PIRL-MS spectra. Data analysis and liquid chromatography coupled with tandem high-resolution mass spectrometry (LC-MS/MS) further allowed us to reduce the molecular feature list to only 18 metabolic lipid markers most strongly involved in this classification. The identified 'metabolite array' was comprised of a variety of phosphatidic and fatty acids, ceramides, and phosphatidylcholine/ethanolamine and could mediate the above-mentioned classification with average sensitivity and specificity values of 94.39 and 98.78%, respectively, at a 95% confidence in prediction probability threshold. Therefore, a rapid and accurate pathology classification of select pediatric brain cancer types from 10 s PIRL-MS analysis using known metabolic biomarkers can now be available to the neurosurgeon. Based on retrospective mining of 'survival' versus 'extent-of-resection' data, we further identified pediatric cancer types that may benefit from actionable 10 s PIRL-MS pathology feedback. In such cases, aggressiveness of the surgical resection can be optimized in a manner that is expected to benefit the patient's overall or progression-free survival. PIRL-MS is a promising tool to drive such personalized decision-making in the operating theater.

Diffusion-Limited Kinetics in Reactive Systems.

A proper representation of chemical kinetics is vital to understanding, modeling, and optimizing many important chemical processes. In liquid and surface phases, where diffusion is slow, the rate at which the reactants diffuse together limits the overall rate of many elementary reactions. Commonly, the textbook Smoluchowski theory is utilized to estimate effective rate coefficients in the liquid phase. On surfaces, modelers commonly resort to much more complex and expensive Kinetic Monte Carlo (KMC) simulations. Here, we extend the Smoluchowski model to allow the diffusing species to undergo chemical reactions and derive analytical formulas for the diffusion-limited rate coefficients for 3D, 2D, and 2D/3D interface cases. With these equations, we are able to demonstrate that when species react faster than they diffuse they can react orders of magnitude faster than predicted by Smoluchowski theory, through what we term "the reactive transport effect". We validate the derived steady-state equations against particle Monte Carlo (PMC) simulations, KMC simulations, and non-steady-state solutions. Furthermore, using PMC and KMC simulations, we propose corrections that agree with all limits and the computed data for the 2D and 2D/3D interface steady-state equations, accounting for unique limitations in the associated derived equations. Additionally, we derive equations to handle couplings between diffusion-limited rate coefficients in reaction networks. We believe these equations should make it possible to run much more accurate mean-field simulations of liquids, surfaces, and liquid-surface interfaces accounting for diffusion limitations and the reactive transport effect.

Implementation and evaluation of sepsis surveillance and decision support in medical ICU and emergency department.

OBJECTIVE: To improve the timely diagnosis and treatment of sepsis many institutions implemented automated sepsis alerts. Poor specificity, time delays, and a lack of actionable information lead to limited adoption by bedside clinicians and no change in practice or clinical outcomes. We aimed to compare sepsis care compliance before and after a multi-year implementation of a sepsis surveillance coupled with decision support in a tertiary care center. DESIGN: Single center before and after study. SETTING: Large academic Medical Intensive Care Unit (MICU) and Emergency Department (ED). POPULATION: Patients 18 years of age or older admitted to *** Hospital MICU and ED from 09/4/2011 to 05/01/2018 with severe sepsis or septic shock. INTERVENTIONS: Electronic medical record-based sepsis surveillance system augmented by clinical decision support and completion feedback. MEASUREMENTS AND MAIN RESULTS: There were 1950 patients admitted to the MICU with the diagnosis of severe sepsis or septic shock during the study period. The baseline characteristics were similar before (N = 854) and after (N = 1096) implementation of sepsis surveillance. The performance of the alert was modest with a sensitivity of 79.9%, specificity of 76.9%, positive predictive value (PPV) 27.9%, and negative predictive value (NPV) 97.2%. There were 3424 unique alerts and 1131 confirmed sepsis patients after the sniffer implementation. During the study period average care bundle compliance was higher; however after taking into account improvements in compliance leading up to the intervention, there was no association between intervention and improved care bundle compliance (Odds ratio: 1.16; 95% CI: 0.71 to 1.89; p-value 0.554). Similarly, the intervention was not associated with improvement in hospital mortality (Odds ratio: 1.55; 95% CI: 0.95 to 2.52; p-value: 0.078). CONCLUSIONS: A sepsis surveillance system incorporating decision support or completion feedback was not associated with improved sepsis care and patient outcomes.

Mass Spectrometry Imaging Reveals a Gradient of Cancer-like Metabolic States in the Vicinity of Cancer Not Seen in Morphometric Margins from Microscopy.

Spatially resolved ambient mass spectrometry imaging methods have gained popularity to characterize cancer sites and their borders using molecular changes in the lipidome. This utility, however, is predicated on metabolic homogeneity at the border, which would create a sharp molecular transition at the morphometric borders. We subjected murine models of human medulloblastoma brain cancer to mass spectrometry imaging, a technique that provides a direct readout of tissue molecular content in a spatially resolved manner. We discovered a distance-dependent gradient of cancer-like lipid molecule profiles in the brain tissue within 1.2 mm of the cancer border, suggesting that a cancer-like state progresses beyond the histologic border, into the healthy tissue. The results were further corroborated using orthogonal liquid chromatography and mass spectrometry (LC-MS) analysis of selected tissue regions subjected to laser capture microdissection. LC-MS/MS analysis for robust identification of the affected molecules implied changes in a number of different lipid classes, some of which are metabolized from the essential docosahexaenoic fatty acid (DHA) present in the interstitial fluid. Metabolic molecular borders are thus not as sharp as morphometric borders, and mass spectrometry imaging can reveal molecular nuances not observed with microscopy. Caution must be exercised in interpreting multimodal imaging results stipulated on a coincidental relationship between metabolic and morphometric borders of cancer, at least within animal models used in preclinical research.

Tailoring Medulloblastoma Treatment Through Genomics: Making a Change, One Subgroup at a Time.

After more than a decade of genomic studies in medulloblastoma, the time has come to capitalize on the knowledge gained and use it to directly improve patient care. Although metastatic and relapsed disease remain poorly understood, much has changed in how we define medulloblastoma, and it has become evident that with conventional therapies, specific groups of patients are currently under- or overtreated. In this review, we summarize the latest insights into medulloblastoma biology, focusing on how genomics is affecting patient stratification, informing preclinical studies of targeted therapies, and shaping the new generation of clinical trials.

Reducing Iatrogenic Pneumothoraces: Using Real-Time Ultrasound Guidance for Pleural Procedures.

OBJECTIVES: Awareness of the impact of bedside ultrasound to reduce iatrogenic pneumothoraces while performing bedside pleural procedures has increased but with little understanding in how ultrasound is used for these procedures. DESIGN AND SETTING: We conducted a retrospective chart review at a tertiary referral center in the United States from January 1, 2014, to March 31, 2017. Our study assessed adverse effect rates between real-time ultrasound-guided and ultrasound-marked thoracenteses and thoracostomy tube placements. PATIENTS: Three-hundred ninety-four ICU patients were included in this study. MEASUREMENTS AND MAIN RESULTS: There was a significant difference in the rate of adverse effects between real-time ultrasound-guided (0.63% [95% CI, 0.11-3.4%]) and ultrasound-marked (6.89% [95% CI, 4.15-11.24%]; p ≤ 0.01) procedures. More specifically, the rate of pneumothoraces was different between the two procedures (0.63% [95% CI, 0.11-3.4%] vs 4.43% [95% CI, 2.35-8.21%]; p = 0.02). In patients mechanically ventilated, there was a significant difference in overall adverse effect rates between groups of ultrasound use (p = 0.01). CONCLUSIONS: The use of real-time ultrasound guidance was associated with a lower rate of iatrogenic pneumothoraces.

Metastatic group 3 medulloblastoma is driven by PRUNE1 targeting NME1-TGF-ß-OTX2-SNAIL via PTEN inhibition.

Genetic modifications during development of paediatric groups 3 and 4 medulloblastoma are responsible for their highly metastatic properties and poor patient survival rates. PRUNE1 is highly expressed in metastatic medulloblastoma group 3, which is characterized by TGF-ß signalling activation, c-MYC amplification, and OTX2 expression. We describe the process of activation of the PRUNE1 signalling pathway that includes its binding to NME1, TGF-ß activation, OTX2 upregulation, SNAIL (SNAI1) upregulation, and PTEN inhibition. The newly identified small molecule pyrimido-pyrimidine derivative AA7.1 enhances PRUNE1 degradation, inhibits this activation network, and augments PTEN expression. Both AA7.1 and a competitive permeable peptide that impairs PRUNE1/NME1 complex formation, impair tumour growth and metastatic dissemination in orthotopic xenograft models with a metastatic medulloblastoma group 3 cell line (D425-Med cells). Using whole exome sequencing technology in metastatic medulloblastoma primary tumour cells, we also define 23 common 'non-synonymous homozygous' deleterious gene variants as part of the protein molecular network of relevance for metastatic processes. This PRUNE1/TGF-ß/OTX2/PTEN axis, together with the medulloblastoma-driver mutations, is of relevance for future rational and targeted therapies for metastatic medulloblastoma group 3.10.1093/brain/awy039_video1awy039media15742053534001.

Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy.

Autophagy is an essential component of innate immunity, enabling the detection and elimination of intracellular pathogens. Legionella pneumophila, an intracellular pathogen that can cause a severe pneumonia in humans, is able to modulate autophagy through the action of effector proteins that are translocated into the host cell by the pathogen's Dot/Icm type IV secretion system. Many of these effectors share structural and sequence similarity with eukaryotic proteins. Indeed, phylogenetic analyses have indicated their acquisition by horizontal gene transfer from a eukaryotic host. Here we report that L. pneumophila translocates the effector protein sphingosine-1 phosphate lyase (LpSpl) to target the host sphingosine biosynthesis and to curtail autophagy. Our structural characterization of LpSpl and its comparison with human SPL reveals high structural conservation, thus supporting prior phylogenetic analysis. We show that LpSpl possesses S1P lyase activity that was abrogated by mutation of the catalytic site residues. L. pneumophila triggers the reduction of several sphingolipids critical for macrophage function in an LpSpl-dependent and -independent manner. LpSpl activity alone was sufficient to prevent an increase in sphingosine levels in infected host cells and to inhibit autophagy during macrophage infection. LpSpl was required for efficient infection of A/J mice, highlighting an important virulence role for this effector. Thus, we have uncovered a previously unidentified mechanism used by intracellular pathogens to inhibit autophagy, namely the disruption of host sphingolipid biosynthesis.

Review of molecular classification and treatment implications of pediatric brain tumors.

PURPOSE OF REVIEW: Brain tumors are the most common solid tumors and leading cause of cancer-related death in children. The advent of large-scale genomics has resulted in a plethora of profiling studies that have mapped the genetic and epigenetic landscapes of pediatric brain tumors, ringing in a new era of precision diagnostics and targeted therapies. In this review, we highlight the most recent findings, focusing on studies published after 2015, and discuss how new evidence is changing the care of children with brain tumors. RECENT FINDINGS: Genome-wide and epigenome-wide profiling data have revealed distinct tumor entities within, virtually, all pediatric brain tumor groups including medulloblastoma; ependymoma; high-grade and low-grade gliomas; atypical teratoid/rhabdoid tumors; and other embryonal tumors, previously called CNS primitive neuroectodermal tumors. Whenever integrated with clinical information, many molecular alterations emerge as powerful prognostic markers and should thus be used to stratify patients and tailor therapies. SUMMARY: Optimal integration of this newly emerging knowledge in a timely and meaningful way into clinical care is a remarkable task and a matter of active debate. The historical morphology-based classification of tumors is being replaced by a genetic-based classification, and the first generation of molecularly informed clinical trials is underway.

Impact of Telemedicine Monitoring of Community ICUs on Interhospital Transfers.

OBJECTIVES: To study the effects of tele-ICU monitoring on interhospital transfers from community-based ICUs to the quaternary care hospital at Mayo Clinic, Rochester, MN. DESIGN: This is a retrospective review of data on interhospital transfers comparing trends prior to tele-ICU implementation to those following implementation. SETTING: Tele-ICU programs are increasingly utilized to fill resource gaps in caring for critically ill patients. How such programs impact population and bed management within a healthcare system are not known. Mayo Clinic serves as quaternary referral care center for hospitals in the region within the Mayo Clinic Health System. In August 2013, we implemented tele-ICU monitoring at six Mayo Clinic Health System hospital ICUs. SUBJECTS: All adult ICU admissions during the study period (preimplementation phase: January 1, 2012, to December 31, 2012; and postimplementation phase: January 1, 2014, to December 31, 2014) in any of the six specified community ICUs were included in the study. MEASUREMENTS AND MAIN RESULTS: Interhospital transfers significantly increased post institution of tele-ICU (p = 0.040) and was attributed primarily to transfer from less specialized ICUs (p = 0.037) as compared with more resource-intensive ICUs (p = 0.88). However, for such patient transfers, there were no significant differences before and after severity of illness scores, ICU mortality, or inhospital mortality. CONCLUSION: In a regional healthcare system, implementation of a tele-ICU program is associated with an increase in interhospital transfers from less resourced ICUs to the referral center, a trend that is not readily explained by increased severity of illness.

Can a Novel ICU Data Display Positively Affect Patient Outcomes and Save Lives?

The aim of this study was to quantify the impact of ProCCESs AWARE, Ambient Clinical Analytics, Rochester, MN, a novel acute care electronic medical record interface, on a range of care process and patient health outcome metrics in intensive care units (ICUs). ProCCESs AWARE is a novel acute care EMR interface that contains built-in tools for error prevention, practice surveillance, decision support and reporting. We compared outcomes before and after AWARE implementation using a prospective cohort and a historical control. The study population included all critically ill adult patients (over 18 years old) admitted to four ICUs at Mayo Clinic, Rochester, MN, who stayed in hospital at least 24 h. The pre-AWARE cohort included 983 patients from 2010, and the post-AWARE cohort included 856 patients from 2014. We analyzed patient health outcomes, care process quality, and hospital charges. After adjusting for patient acuity and baseline demographics, overall in-hospital and ICU mortality odds ratios associated with AWARE intervention were 0.45 (95% confidence interval 0.30 to 0.70) and 0.38 (0.22, 0.66). ICU length of stay decreased by about 50%, hospital length of stay by 37%, and total charges for hospital stay by 30% in post AWARE cohort (by $43,745 after adjusting for patient acuity and demographics). Better organization of information in the ICU with systems like AWARE has the potential to improve important patient outcomes, such as mortality and length of stay, resulting in reductions in costs of care.

Posterior fossa ependymoma: current insights.

BACKGROUND: Ependymoma is the third most common malignant tumor of the posterior fossa and is a major cause of neurological morbidity and mortality in children. Current treatments, particularly surgery and external beam irradiation result in relatively poor outcomes with significant neurological and cognitive sequelae from treatment. Historical approaches have considered all ependymomas as similar entities based on their morphological appearance. RESULTS: Recent advances in genomics and epigenetics have revealed, however, that ependymomas from different CNS locations represent distinct entities. Moreover, ependymoma of the posterior fossa, the most common location in children, is actually comprised of two distinct molecular variants. These two variants have marked differences in demographics, transcriptomes, structure, methylation patterns, and clinical outcomes. This allows for the development of new biology-based clinical risk stratification, which can both prioritize patients for de-escalation of therapy and identify those who will benefit from novel therapeutic strategies. Indeed, the identification of these two variants allows an opportunity for robust preclinical modeling for development of novel therapeutic strategies. CONCLUSIONS: Herein, we have summarized our current clinical approach to diagnosis and treatment of posterior fossa ependymoma, recent advances in understanding the biology of posterior fossa ependymoma and how these new insights can be translated into the clinic to form the basis of the next generation of clinical trials.

The Legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments.

Legionella pneumophila uses aquatic protozoa as replication niche and protection from harsh environments. Although L. pneumophila is not known to have a circadian clock, it encodes homologues of the KaiBC proteins of Cyanobacteria that regulate circadian gene expression. We show that L. pneumophila kaiB, kaiC and the downstream gene lpp1114, are transcribed as a unit under the control of the stress sigma factor RpoS. KaiC and KaiB of L. pneumophila do not interact as evidenced by yeast and bacterial two-hybrid analyses. Fusion of the C-terminal residues of cyanobacterial KaiB to Legionella KaiB restores their interaction. In contrast, KaiC of L. pneumophila conserved autophosphorylation activity, but KaiB does not trigger the dephosphorylation of KaiC like in Cyanobacteria. The crystal structure of L. pneumophila KaiB suggests that it is an oxidoreductase-like protein with a typical thioredoxin fold. Indeed, mutant analyses revealed that the kai operon-encoded proteins increase fitness of L. pneumophila in competitive environments, and confer higher resistance to oxidative and sodium stress. The phylogenetic analysis indicates that L. pneumophila KaiBC resemble Synechosystis KaiC2B2 and not circadian KaiB1C1. Thus, the L. pneumophila Kai proteins do not encode a circadian clock, but enhance stress resistance and adaption to changes in the environments.

Development and Implementation of an Acute Kidney Injury Remote Patient Monitoring Program: Research Letter.

Acute kidney injury (AKI) survivors have a dynamic posthospital course which warrants close monitoring. Remote patient monitoring (RPM) could be used to improve quality and efficiency of AKI survivor care. Objective: The objective of this report was to describe the development and preliminary feasibility of an AKI RPM program launched in October 2021. Setting: Academic medical center. Patients: Patients enrolled in the AKI RPM program were those who experienced AKI during a hospitalization and underwent nephrology consultation. Measurements/Methods: At enrollment, patients were provided with home monitoring technology and underwent weekly laboratory assessments. Nurses evaluated the data daily and adhered to prespecified protocols for management and escalation of care if needed. Results: Twenty patients were enrolled in AKI RPM in the first 5 months. Median duration of program participation was 36 (31, 40) days. Eight patients (40%) experienced an unplanned readmission, or an emergency department visit, half (N = 4) of which were attributed to AKI and related circumstances. Of the 9 postgraduation survey respondents, all were satisfied with the RPM program and 89% would recommend RPM to other patients with similar health conditions. Limitations: Acute kidney injury RPM was made possible by the existing infrastructure in our integrated health system and the robust resources available in the Mayo Clinic Center for Digital Health. Such infrastructure may not be universally available which could limit scale and generalizability of such a program. Conclusions: Remote patient monitoring can offer a unique opportunity to bridge the care transition from hospital to home and increase access to quality care for the AKI survivors.

Les survivants d'un épisode d'insuffisance rénale aiguë (IRA) ont un parcours post-hospitalier dynamique qui justifie une surveillance étroite. La télésurveillance des patients (TSP) pourrait être employée pour améliorer la qualité et l'efficacité des soins pour les survivants de l'IRA. Objectif: L'objectif de ce rapport était de décrire le développement et la faisabilité préliminaire d'un programme de TSP-IRA (télésurveillance des patients atteints d'IRA) en octobre 2021. Cadre: Centre médical universitaire. Sujets: Les patients inscrits au programme de TSP-IRA étaient des patients qui avaient vécu un épisode d'IRA lors d'une hospitalisation et obtenu une consultation en néphrologie. Mesures et méthodologie: Au moment de l'inclusion, les patients ont reçu un dispositif de surveillance à domicile et se sont soumis à des évaluations de laboratoire hebdomadaires. Les infirmières ont évalué les données quotidiennement et ont respecté des protocoles prédéfinis pour la gestion et l'escalade des soins si nécessaire. Résultats: Vingt patients ont été inclus dans le programme de TSP-IRA au cours des cinq premiers mois. La durée médiane de participation au programme était de 36 (31, 40) jours. Huit patients (40%) ont dû être réadmis de façon non planifiée ou ont dû faire une visite aux urgences; pour la moitié d'entre eux (N = 4) en raison de l'IRA et de circonstances connexes. Parmi les neuf répondants qui ont répondu au sondage à la complétion du programme, tous se sont dits satisfaits du programme de TSP et 89% le recommanderaient à d'autres patients ayant des problèmes de santé similaires. Limites: Le programme de TSP-IRA a été rendu possible grâce à l'infrastructure existante dans notre système de santé intégré et aux ressources robustes disponibles au Mayo Clinic Center for Digital Health. Une telle infrastructure n'est peut-être pas universellement disponible, ce qui pourrait limiter l'ampleur et la généralisabilité d'un tel programme. Conclusion: La TSP peut offrir une occasion unique de faciliter la transition des soins entre l'hôpital et le domicile et d'accroître l'accès à des soins de qualité pour les survivants d'un épisode d'IRA.

Domain cross-talk during effector binding to the multidrug binding TTGR regulator.

A major mechanism of antibiotic resistance in bacteria is the active extrusion of toxic compounds through membrane-bound efflux pumps. The TtgR protein represses transcription of ttgABC, a key efflux pump in Pseudomonas putida DOT-T1E capable of extruding antibiotics, solvents, and flavonoids. TtgR contains two distinct and overlapping ligand binding sites, one is broad and contains mainly hydrophobic residues, whereas the second is deep and contains polar residues. Mutants in the ligand binding pockets were generated and characterized using electrophoretic mobility shift assays, isothermal titration calorimetry, and promoter expression. Several mutants were affected in their response to effectors in vitro: mutants H70A, H72A, and R75A did not dissociate from promoter DNA in the presence of chloramphenicol. Other mutants exhibited altered binding to the operator: L66A and L66AV96A mutants bound 3- and 15-fold better than the native protein, whereas the H67A mutant bound with 3-fold lower affinity. In vivo expression assays using a fusion of the promoter of ttgA to lacZ and antibiotic tolerance correlated with the in vitro observations, namely that mutant H67A leads to increased basal expression levels and enhances antibiotic tolerance, whereas mutants L66A and L66AV96A exhibit lower basal expression levels and decreased resistance to antibiotics. The crystal structure of TtgR H67A was resolved. The data provide evidence for the inter-domain communication that is predicted to be required for the transmission of the effector binding signal to the DNA binding domain and provide important information to understand TtgR/DNA/effector interactions.