YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression.

The DNA guanine quadruplexes (G4) play important roles in multiple cellular processes, including DNA replication, transcription and maintenance of genome stability. Here, we showed that Yin and Yang 1 (YY1) can bind directly to G4 structures. ChIP-seq results revealed that YY1-binding sites overlap extensively with G4 structure loci in chromatin. We also observed that the dimerization of YY1 and its binding with G4 structures contribute to YY1-mediated long-range DNA looping. Displacement of YY1 from G4 structure sites disrupts substantially the YY1-mediated DNA looping. Moreover, treatment with G4-stabilizing ligands modulates the expression of not only those genes with G4 structures in their promoters, but also those associated with distal G4 structures that are brought to close proximity via YY1-mediated DNA looping. Together, we identified YY1 as a DNA G4-binding protein, and revealed that YY1-mediated long-range DNA looping requires its dimerization and occurs, in part, through its recognition of G4 structure.

Response and resistance to CDK12 inhibition in aggressive B-cell lymphomas.

Despite significant progress in the treatment of patients with diffuse large B-cell lymphoma (DLBCL) and mantle cell lymphoma (MCL), the prognosis of patients with relapsed disease remains poor due to the emergence of drug resistance and subsequent disease progression. Identification of novel targets and therapeutic strategies for these diseases represents an urgent need. Here, we report that both MCL and DLBCL are exquisitely sensitive to transcription-targeting drugs, in particular THZ531, a covalent inhibitor of cyclin-dependent kinase 12 (CDK12). By implementing pharmacogenomics and a cell-based drug screen, we found that THZ531 leads to inhibition of oncogenic transcriptional programs, especially the DNA damage response pathway, MYC target genes and the mTOR-4EBP1-MCL-1 axis, contributing to dramatic lymphoma suppression in vitro. We also identified de novo and established acquired THZ531-resistant lymphoma cells conferred by over-activation of the MEK-ERK and PI3K-AKT-mTOR pathways and upregulation of multidrug resistance-1 (MDR1) protein. Of note, EZH2 inhibitors reversed resistance to THZ531 by competitive inhibition of MDR1 and, in combination with THZ531, synergistically inhibited MCL and DLBCL growth in vitro. Our study indicates that CDK12 inhibitors, alone or together with EZH2 inhibitors, offer promise as novel effective approaches for difficult-to-treat DLBCL and MCL.

Correcting Finger Counting to Snellen Acuity.

In this paper, the authors describe an online tool with which to convert and thus quantify count finger measurements of visual acuity into Snellen equivalents. It is hoped that this tool allows for the re-interpretation of retrospectively collected data that provide visual acuity in terms of qualitative count finger measurements.

Drug-related mitochondrial optic neuropathies.

BACKGROUND: There is a group of optic neuropathies of either genetic or acquired origin characterized by similar clinical manifestations with preferential involvement of the papillomacular bundle (PMB). PMB fibers are most susceptible to injury as they are small, unmyelinated, and have high-energy demands. These optic neuropathies share a presumed common pathophysiology of mitochondrial dysfunction. EVIDENCE ACQUISITION: A variety of medications cause optic neuropathy by interfering with mitochondrial function. The evidence linking these therapeutic agents as a cause of mitochondrial optic neuropathy (MON) is well established in some and less certain in others. The differential diagnosis includes other optic nerve disorders producing bilateral, symmetric visual loss, including certain nutritional deficiencies, toxins, and genetic diseases. RESULTS: Ethambutol, chloramphenicol, linezolid, erythromycin, streptomycin, and antiretroviral drugs can cause drug-related MON. In many cases, drug toxicity is dose and duration dependent, and discontinuation of the drug in a timely manner can lead to significant visual recovery. CONCLUSIONS: Mitochondrial optic neuropathies are increasingly recognized as a spectrum of conditions that reach a similar end point by compromising a common pathway of mitochondrial dysfunction. Clinicians should be aware of drugs that can cause a MON. Prompt recognition of this association is critical in preventing irreversible, profound visual loss.

Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues.

Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4CRBN ligase, have been mostly discovered serendipitously. We recently reported a trans-labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 trans-labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4CRBN glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.

Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders.

Small molecules that induce protein-protein interactions to exert proximity-driven pharmacology such as targeted protein degradation are a powerful class of therapeutics1-3. Molecular glues are of particular interest given their favorable size and chemical properties and represent the only clinically approved degrader drugs4-6. The discovery and development of molecular glues for novel targets, however, remains challenging. Covalent strategies could in principle facilitate molecular glue discovery by stabilizing the neo-protein interfaces. Here, we present structural and mechanistic studies that define a trans-labeling covalent molecular glue mechanism, which we term "template-assisted covalent modification". We found that a novel series of BRD4 molecular glue degraders act by recruiting the CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). BRD4BD2, in complex with DCAF16, serves as a structural template to facilitate covalent modification of DCAF16, which stabilizes the BRD4-degrader-DCAF16 ternary complex formation and facilitates BRD4 degradation. A 2.2 Å cryo-electron microscopy structure of the ternary complex demonstrates that DCAF16 and BRD4BD2 have pre-existing structural complementarity which optimally orients the reactive moiety of the degrader for DCAF16Cys58 covalent modification. Systematic mutagenesis of both DCAF16 and BRD4BD2 revealed that the loop conformation around BRD4His437, rather than specific side chains, is critical for stable interaction with DCAF16 and BD2 selectivity. Together our work establishes "template-assisted covalent modification" as a mechanism for covalent molecular glues, which opens a new path to proximity driven pharmacology.

Exploring Methods of Targeting Histone Methyltransferases and Their Applications in Cancer Therapeutics.

Histone methyltransferases (HMTs) are enzymes that catalyze the methylation of lysine or arginine residues of histone proteins, a key post-translational modification (PTM). Aberrant expression or activity of these enzymes can lead to abnormal histone methylation of cancer-related genes and thus promote tumorigenesis. Histone methyltransferases have been implicated in chemotherapeutic resistance and immune stimulation, making these enzymes potential therapeutic targets of interest, and chemically targeting these proteins provides an avenue for novel drug development in cancer therapy. This Review aims to discuss the evolution of chemical approaches that have emerged in the past five years to design probes targeting these enzymes, including inhibition through noncovalent inhibitors, covalent inhibitors, and targeted protein degradation through proteolysis targeting chimeras (PROTACs). This Review also highlights how these compounds have been used to study the myriad of HMT functions in cancer progression and treatment response. The recent advancement of some of these drugs into human clinical investigation and even to regulatory approval highlights HMTs as a promising class of targets for chemical intervention and novel therapy development.

Axonal degeneration in peripheral nerves in a case of Leber hereditary optic neuropathy.

BACKGROUND: Leber hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) genetic disorder characterized by profound bilateral loss of central vision due to selective loss of retinal ganglion cells. Most patients with LHON do not have complaints related to the peripheral nervous system. We investigated possible qualitative and quantitative histological changes in the peripheral nerve of a patient with LHON as compared to normal controls. METHODS: Brachial plexus specimens were obtained at necropsy from a patient with LHON carrying the 3460/ND1 mtDNA mutation and age-matched controls without known history of neurological disease. The nerves were evaluated by light microscope coupled to a digital camera-based morphometric analysis and electron microscopy. RESULTS: Extensive axonal degeneration of the large heavily myelinated fibers was found in the brachial plexus from the patient with LHON. In LHON nerve fascicles, we counted over 10 times as many degenerated profiles as found in the control nerve fascicles. CONCLUSIONS: Microscopic examination of the brachial plexus in the patient with LHON clearly demonstrated a significant pattern of neurodegeneration. Our study suggests that peripheral neuropathy may be a subclinical feature associated with LHON.

Low-density lipoprotein receptor-related protein is decreased in optic neuropathy of Alzheimer disease.

BACKGROUND: Alzheimer disease (AD) is associated with optic nerve degeneration, yet the underlying pathophysiology of this disease and the optic nerve disorder remain poorly understood. Low-density lipoprotein receptor-related protein (LRP) is implicated in the pathogenesis of AD by mediating the transport of amyloid-ß (Aß) out of the brain into the systemic circulation. As a key player in the reaction to central nervous system injury, astrocytes associate with LRP in AD. This study investigates the role of LRP and astrocytes in the pathogenesis of AD optic neuropathy. METHODS: To investigate the role of LRP and astrocytes in the pathogenesis of AD optic neuropathy, we conducted immunohistochemical studies on postmortem optic nerves in AD patients (n = 11) and age-matched controls (n = 10) to examine the presence of LRP. Quantitative analyses using imaging software were used to document the extent of LRP in neural tissues. Axonal integrity was assessed by performing immunohistochemistry on the subjects' optic nerves with an antibody to neurofilament (NF) protein. Double-immunofluorescence labeling was performed to investigate whether LRP colocalized with astrocytes, expressing glial fibrillary acidic protein. RESULTS: LRP expression was decreased in AD optic nerves compared to that in controls (P < 0.001). LRP immunoreactivity was observed in the microvasculature and perivascularly in close proximity to the astrocytic processes. Colocalization of LRP in the astrocytes of optic nerves was also demonstrated. The presence of optic neuropathy was confirmed in the AD optic nerves by demonstrating greatly reduced immunostaining for NF protein as compared to controls. CONCLUSIONS: The reduction of LRP in the AD degenerative optic nerves supports the hypothesis that LRP may play a role in the pathophysiology of AD optic neuropathy.

Transcriptional programming drives Ibrutinib-resistance evolution in mantle cell lymphoma.

Ibrutinib, a bruton's tyrosine kinase (BTK) inhibitor, provokes robust clinical responses in aggressive mantle cell lymphoma (MCL), yet many patients relapse with lethal Ibrutinib-resistant (IR) disease. Here, using genomic, chemical proteomic, and drug screen profiling, we report that enhancer remodeling-mediated transcriptional activation and adaptive signaling changes drive the aggressive phenotypes of IR. Accordingly, IR MCL cells are vulnerable to inhibitors of the transcriptional machinery and especially so to inhibitors of cyclin-dependent kinase 9 (CDK9), the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Further, CDK9 inhibition disables reprogrammed signaling circuits and prevents the emergence of IR in MCL. Finally, and importantly, we find that a robust and facile ex vivo image-based functional drug screening platform can predict clinical therapeutic responses of IR MCL and identify vulnerabilities that can be targeted to disable the evolution of IR.

Posterior ischemic optic neuropathy: Perioperative risk factors.

Perioperative posterior ischemic optic neuropathy (PION) is a rare but devastating condition. Visual impairment is commonly bilateral, profound, and irreversible. The most frequently associated triggering events are spine surgeries, other orthopedic surgeries, cardiac bypass surgeries, and radical neck dissection. The etiology is multifactorial. The most commonly reported risk factors are severe and prolonged hypotension, anemia, hemodilution, orbital and periorbital edema, direct orbital compression by prone position, and abnormal autoregulation. This review discusses the current literature on perioperative PION and includes a study conducted by our group to investigate the perioperative risk factors of PION in order to better understand the pathogenesis and help identify high-risk patients. Our results provide further corroborating evidence that PION is associated with spinal, cardiovascular, and abdominal surgeries, longer duration of procedure, and facial edema. Anemia and chronic hypertension are frequent risk factors. Treatment for perioperative PION is uncertain and depends largely on the immediate reversal of hemodynamic alterations. Hence, it is important to identify patients at risk and accordingly take prophylactic measures to prevent its occurrence. Optimizing hemoglobin levels, hemodynamic status, and tissue oxygenation is crucial.

Receptor for advanced glycation end products is upregulated in optic neuropathy of Alzheimer's disease.

Although Alzheimer's disease (AD) has been shown to be associated with a true primary optic neuropathy, the underlying pathophysiology of this disease and in particular the optic nerve disorder is still poorly understood. The receptor for advanced glycation end products (RAGE) has been implicated in the pathogenesis of AD by mediating the transport of plasma amyloid-beta into the brain. Once ligated, RAGE can play a role in signal transduction, leading to amplification and perpetuation of inflammatory processes. As a key player in the reaction to CNS injury, astrocytes have been shown to associate with RAGE in a number of diseases, including AD. To investigate the role of RAGE and astrocytes in the pathogenesis of AD optic neuropathy, we conducted immunohistochemical studies to examine the presence of RAGE in donor eyes from patients with AD (n = 10) and controls (n = 3). Both qualitative observation and quantitative analyses using imaging software were used to document the extent of RAGE in the neural tissues. The intensity and extent of RAGE expression was more prominent in AD nerves compared to controls (P < 0.05). The RAGE immunoreactivity was observed in the microvasculature and in close proximity to astrocytic processes. While RAGE immunoreactivity increased with age, the increase was more precipitous in the AD group compared to the controls. The up-regulation of RAGE in the AD optic nerves indicates that RAGE may play a role in the pathophysiology of AD optic neuropathy.

Vitreo-papillary adhesion in macular hole and macular pucker.

PURPOSE: Vitreo-macular pathology may be influenced by vitreo-papillary adhesion (VPA). Optical coherence tomography/scanning laser ophthalmoscopy (OCT/SLO) was used to identify VPA in full-thickness macular hole, lamellar hole, and macular pucker (MP). METHODS: Ultrasonography and OCT/SLO were performed in 55 subjects: 16 with macular hole, 11 with lamellar hole, and 28 with MP. The main outcome measures were the presence of posterior vitreous detachment by ultrasound, and the findings of VPA and intraretinal cysts by OCT/SLO. RESULTS: Posterior vitreous detachment was detected by ultrasound in 26/28 (92.9%) eyes with MP, 6/11 (54.5%) eyes with lamellar hole (P < 0.05), and 4/16 (25%) eyes with macular hole (P < 0.00001). Optical coherence tomography/scanning laser ophthalmoscopy detected VPA in 14/16 (87.5%) macular hole eyes, 4/11 (36.4%) lamellar hole eyes (P < 0.05), and 5/28 (17.9%) MP eyes (P < 0.00005). Intraretinal cysts were present in 4/5 (80%) MP eyes with VPA but only 1/23 (4.3%) MP eyes without VPA (P < 0.005). CONCLUSION: Vitreo-papillary adhesion was significantly more common in full-thickness macular hole than lamellar hole or MP. When present in MP, VPA was frequently associated with intraretinal cysts. Hence, VPA may have an important influence on the vectors of force at the vitreo-retinal interface inducing holes and cysts.

Value of medical history in ophthalmology: A study of diagnostic accuracy.

PURPOSE: This study aimed to demonstrate the value of the chief compliant and patient history to accurately diagnose patient pathology without requiring ocular examination or imaging in an outpatient neuro-ophthalmology clinic. METHODS: We prospectively evaluated 115 consecutive patients at our institution from January to April 2009. The attending neuro-ophthalmologist committed to a single most likely diagnosis while solely being exposed to patient demographic information (age, gender, race) and chief complaint, but was otherwise blinded to ocular examination or imaging. The validity of the initial diagnosis was assessed by further acquiring subjective and objective findings and the percentage of correct diagnoses was determined. RESULTS: Patient cases were categorized based on the neuro-ophthalmologic localization of the final diagnoses: afferent nervous system, central nervous system (CNS), efferent nervous system, orbital system, and pupillary system. Correct diagnoses by chief complaint and patient history were 84%, 100%, 86%, 80%, 50% and 100% for afferent, central, efferent, orbit, pupil, and other neuro-ophthalmic diseases, respectively. Over half the cases were correctly diagnosed by chief complaint alone, which improved to 88% when combined with the patient history. CONCLUSIONS: A simple combination of patient history and chief complaint predicts an overall diagnostic accuracy in approximately 90% of cases. Our study demonstrates the remarkable diagnostic value of patient history in neuro-ophthalmologic clinic practice.

Covariance based outlier detection with feature selection.

The present covariance based outlier detection algorithm selects from a candidate set of feature vectors that are best at identifying outliers. Features extracted from biomedical and health informatics data can be more informative in disease assessment and there are no restrictions on the nature and number of features that can be tested. But an important challenge for an algorithm operating on a set of features is for it to winnow the effective features from the ineffective ones. The powerful algorithm described in this paper leverages covariance information from the time series data to identify features with the highest sensitivity for outlier identification. Empirical results demonstrate the efficacy of the method.

Efficient Blockwise Permutation Tests Preserving Exchangeability.

In this paper, we present a new blockwise permutation test approach based on the moments of the test statistic. The method is of importance to neuroimaging studies. In order to preserve the exchangeability condition required in permutation tests, we divide the entire set of data into certain exchangeability blocks. In addition, computationally efficient moments-based permutation tests are performed by approximating the permutation distribution of the test statistic with the Pearson distribution series. This involves the calculation of the first four moments of the permutation distribution within each block and then over the entire set of data. The accuracy and efficiency of the proposed method are demonstrated through simulated experiment on the magnetic resonance imaging (MRI) brain data, specifically the multi-site voxel-based morphometry analysis from structural MRI (sMRI).

Headache and whiteout vision as the presenting symptoms in a case of Takayasu retinopathy.

PURPOSE: To report a case of Takayasu retinopathy presenting as chronic headache and whiteout of vision. METHODS: A case report of a 28-year-old woman with no medical history diagnosed with Takayasu retinopathy after a complete ophthalmologic examination, including widefield fluorescein angiography. RESULTS: Dilated fundus examination revealed sharp margins in both eyes and mildly attenuated arterioles and distended veins. The peripheral examination was significant for several white-centered intraretinal hemorrhages. A widefield fluorescein angiogram showed numerous small microaneurysms in the periphery. A computer tomography angiogram of the chest showed central wall thickening of the aortic arch, proximal branch vessels of the aortic arch, including left common carotid and right common carotid, and middle lower lobe of the right pulmonary artery, all of which were consistent with the diagnosis of Takayasu disease. The patient underwent cardiovascular bypass surgery and her ocular symptoms resolved. CONCLUSION: Up to one third of patients with Takayasu disease experience visual disturbances, and as a result, ophthalmologists may be the first physicians to encounter and diagnose this condition. The various stages of Takayasu retinopathy are characterized by dilation of small vessels, capillary microaneurysm formation, and development of arterial-venous anastomoses. The initial clinical presentation of Takayasu disease can be varied and nonspecific, therefore a high index of clinical suspicion is essential for diagnosis.