Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens

Millions of putative transcriptional regulatory elements (TREs) have been cataloged in the human genome, yet their functional relevance in specific pathophysiological settings remains to be determined. This is critical to understand how oncogenic transcription factors (TFs) engage specific TREs to impose transcriptional programs underlying malignant phenotypes. Here, we combine cutting edge CRISPR screens and epigenomic profiling to functionally survey ≈15,000 TREs engaged by estrogen receptor (ER). We show that ER exerts its oncogenic role in breast cancer by engaging TREs enriched in GATA3, TFAP2C, and H3K27Ac signal. These TREs control critical downstream TFs, among which TFAP2C plays an essential role in ER-driven cell proliferation. Together, our work reveals novel insights into a critical oncogenic transcription program and provides a framework to map regulatory networks, enabling to dissect the function of the noncoding genome of cancer cells.

Cancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens

YAP is a key transcriptional co-activator of TEADs, it regulates cell growth and is frequently activated in cancer. In Malignant Pleural Mesothelioma (MPM), YAP is activated by loss-of-function mutations in upstream components of the Hippo pathway, while, in Uveal Melanoma (UM), YAP is activated in a Hippo-independent manner. To date, it is unclear if and how the different oncogenic lesions activating YAP impact its oncogenic program, which is particularly relevant for designing selective anti-cancer therapies. Here we show that, despite YAP being essential in both MPM and UM, its interaction with TEAD is unexpectedly dispensable in UM, limiting the applicability of TEAD inhibitors in this cancer type. Systematic functional interrogation of YAP regulatory elements in both cancer types reveals convergent regulation of broad oncogenic drivers in both MPM and UM, but also strikingly selective programs. Our work reveals unanticipated lineage-specific features of the YAP regulatory network that provide important insights to guide the design of tailored therapeutic strategies to inhibit YAP signaling across different cancer types.

Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion

Liver cancer susceptibility varies amongst humans and between experimental animal models because of multiple genetic and epigenetic factors. The molecular characterization of such susceptibilities has the potential to enhance cancer risk assessment of xenobiotic exposures and disease prevention strategies. Here, using DNase I hypersensitivity mapping coupled with transcriptomic profiling, we investigate perturbations in cis-acting gene regulatory elements associated with the early stages of phenobarbital (PB)-mediated liver tumor promotion in susceptible versus resistant mouse strains (B6C3F1 versus C57BL/6J). Integrated computational analyses of strain-selective changes in liver chromatin accessibility underlying PB response reveal differential epigenetic regulation of molecular pathways associated with PB-mediated tumor promotion, including Wnt/β-catenin signaling. Complementary transcription factor motif analyses reveal mouse strain-selective gene regulatory networks and a novel role for Stat, Smad, and Fox transcription factors in the early stages of PB-mediated tumor promotion. Mapping perturbations in cis-acting gene regulatory elements provides novel insights into the molecular basis for susceptibility to xenobiotic-induced rodent liver tumor promotion and has the potential to enhance mechanism-based cancer risk assessments of xenobiotic exposures.

Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq

D-cycloserine (DCS) has been shown to be effective in facilitating fear extinction in animal and human studies, however the precise mechanisms whereby the co-administration of DCS and behavioural fear extinction reduce fear are still unclear. This study investigated the molecular mechanisms of intrahippocampally administered D-cycloserine in facilitating fear extinction in a contextual fear conditioning animal model. Male Sprague Dawley rats (n = 120) were grouped into four experimental groups (n = 30) based on fear conditioning and intrahippocampal administration of either DCS or saline. The light/dark avoidance test was used to differentiate maladapted (MA) (anxious) from well-adapted (WA) (not anxious) subgroups. RNA extracted from the left dorsal hippocampus was used for RNA sequencing and gene expression data was compared between six fear-conditioned + saline MA (FEAR + SALINE MA) and six fear-conditioned + DCS WA (FEAR + DCS WA) animals. Of the 424 significantly downregulated and 25 significantly upregulated genes identified in the FEAR + DCS WA group compared to the FEAR + SALINE MA group, 121 downregulated and nine upregulated genes were predicted to be relevant to fear conditioning and anxiety and stress-related disorders. The majority of downregulated genes transcribed immune, proinflammatory and oxidative stress systems molecules. These molecules mediate neuroinflammation and cause neuronal damage. DCS also regulated genes involved in learning and memory processes, and genes associated with anxiety, stress-related disorders and co-occurring diseases (e.g., cardiovascular diseases, digestive system diseases and nervous system diseases). Identifying the molecular underpinnings of DCS-mediated fear extinction brings us closer to understanding the process of fear extinction.

Protein destabilization underlies pathogenic missense mutations in ARID1B

ARID1B is a SWI/SNF subunit frequently mutated in human Coffin-Siris syndrome (CSS) and it is necessary for proliferation of ARID1A mutant cancers. While most CSS ARID1B aberrations introduce frameshifts or stop codons, the functional consequence of missense mutations found in ARID1B is unclear. We here perform saturated mutagenesis screens on ARID1B and demonstrate that protein destabilization is the main mechanism associated with pathogenic missense mutations in patients with Coffin-Siris Syndrome.

The transcription factor ZNF469 regulates collagen production in liver fibrosis

Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.

Genome assembly of the bearded iris, Iris pallida Lam

Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess antioxidant, anti-inflammatory and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04-Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.

The transcription factor ZNF469 regulates collagen production in liver fibrosis

Metabolic dysfunction-associated steatotic liver disease (MASLD) - characterized by excess accumulation of fat in the liver - now affects one-third of the world's population. As MASLD progresses, extracellular matrix components including collagen accumulate in the liver, causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply characterized cohort of patients spanning the full histopathologic spectrum of MASLD. CRISPR-based genetic KO of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation, we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of MASLD-associated liver fibrosis.

A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction

Sickle cell disease (SCD) is a prevalent, life-threatening condition attributable to a heritable mutation in β-hemoglobin. Therapeutic induction of fetal hemoglobin (HbF) can ameliorate disease complications and has been intently pursued. However, safe and effective small-molecule inducers of HbF remain elusive. We report the discovery of dWIZ-1 and dWIZ-2, molecular glue degraders of the WIZ transcription factor that robustly induce HbF in erythroblasts. Phenotypic screening of a cereblon (CRBN)-biased chemical library revealed WIZ as a previously unknown repressor of HbF. WIZ degradation is mediated by recruitment of WIZ(ZF7) to CRBN by dWIZ-1, as resolved by crystallography of the ternary complex. Pharmacological degradation of WIZ was well tolerated and induced HbF in humanized mice and cynomolgus monkeys. These findings establish WIZ degradation as a globally accessible therapeutic strategy for SCD.

IL-26 Potentiates Type 2 Skin Inflammation in the Presence of IL-1β

Atopic dermatitis (AD) is a debilitating inflammatory skin disorder. Biologics targeting the IL-4/IL-13 axis are effective in AD, but there is still a large proportion of patients who do not respond to IL-4R blockade. Further exploration of potentially pathogenic T-cell-derived cytokines in AD may lead to new effective treatments. This study aimed to investigate the downstream effects of IL-26 on skin in the context of type 2 skin inflammation. We found that IL-26 alone exhibited limited inflammatory activity in the skin. However, in the presence of IL-1β, IL-26 potentiated the secretion of TSLP, CXCL1, and CCL20 from human epidermis through Jak/signal transducer and activator of transcription signaling. Moreover, in an in vivo AD-like skin inflammation model, IL-26 exacerbated skin pathology and locally increased type 2 cytokines, most notably of IL13 in skin T helper cells. Neutralization of IL-1β abrogated IL-26-mediated effects, indicating that the presence of IL-1β is required for full IL-26 downstream action in vivo. These findings suggest that the presence of IL-1β enables IL-26 to be a key amplifier of inflammation in the skin. As such, IL-26 may contribute to the development and pathogenesis of inflammatory skin disorders such as AD.

Biological Psychiatry Congress 2015

<p><strong>List of Abstract Titles and authors:<br /></strong></p><p><strong>1. Psychosis: A matter of mental effort?</strong></p><p>M Borg, Y Y van der Zee, J H Hsieh, H Temmingh, D J Stein, F M Howells</p><p><strong>2.In search of an affordable, effective post-discharge intervention: A randomised control trial assessing the influence of a telephone-based intervention on readmissions for patients with severe mental illness in a developing country</strong></p><p><strong></strong>U A Botha, L Koen, M Mazinu, E Jordaan, D J H Niehaus</p><p><strong>3. The effect of early abstinence from long-term methamphetamine use on brain metabolism using 1H-magnetic resonance spectro-scopy (1H-MRS)</strong></p><p>A Burger, S Brooks, D J Stein, F M Howells</p><p><strong>4. The effect of <em>in utero exposure </em>to methamphetamine on brain metabolism in childhood using 1H-magnetic resonance spectroscopy (1H-MRS)</strong></p><p>A Burger, A Roos, M Kwiatkowski, D J Stein, K A Donald, F M Howells</p><p><strong>5. A prospective study of clinical, biological and functional aspects of outcome in first-episode psychosis: The EONKCS Study</strong></p><p><strong></strong>B Chiliza, L Asmal, R Emsley</p><p><strong>6. Stimulants as cognitive enhancers - perceptions v. evidence in a very real world</strong></p><p><strong></strong>H M Clark</p><p><strong>7. Pharmacogenomics in antipsychotic drugs</strong></p><p><strong></strong>Ilse du Plessis</p><p><strong>8. Serotonin in anxiety disorders and beyond</strong></p><p><strong></strong>Ilse du Plessis</p><p><strong>9. HIV infection results in ventral-striatal reward system hypo-activation during cue processing</strong></p><p><strong></strong>S du Plessis, M Vink, J A Joska, E Koutsilieri, A Bagadia, D J Stein, R Emsley</p><p><strong>10. Disease progression in schizophrenia: Is the illness or the treatment to blame?</strong></p><p>R Emsley, M J Sian</p><p><strong>11. Serotonin transporter variants play a role in anxiety sensitivity in South African adolescents</strong></p><p> S M J Hemmings, L I Martin, L van der Merwe, R Benecke, K Domschke, S Seedat</p><p><strong>12. Iron deficiency in two children diagnosed with multiple sclerosis: Report on whole exom sequencing</strong></p><p><strong></strong>S Janse van Rensburg, R van Toorn, J F Schoeman, A Peeters, L R Fisher, K Moremi, M J Kotze</p><p><strong>13. Benzodiazepines: Practical pharmacokinetics</strong></p><p><strong></strong>P Joubert</p><p><strong>14. What to consider when prescribing psychotropic medications</strong></p><p><strong></strong>G Lippi</p><p><strong>15. Current prescribing practices for obsessive-compulsive disorder in South Africa: Controversies and consensus</strong></p><p><strong></strong>C Lochner, L Taljaard, D J Stein</p><p><strong>16. Correlates of emotional and behavioural problems in children with preinatally acquired HIV in Cape Town, South Africa</strong></p><p><strong></strong>K-A Louw, N Phillips, JIpser, J Hoare</p><p><strong>17. The role of non-coding RNAs in fear extinction</strong></p><p><strong></strong>S Malan-Muller, L Fairbairn, W M U Daniels, M J S Dashti, E J Oakleley, M Altorfer, J Harvey, S Seedat, J Gamieldien, S M J Hemmings</p><p><strong>18. An analysis of the management og HIV-mental illness comorbidity at the psychiatric unit of the Dr George Mukhari Academic Hospital</strong></p><p><strong></strong>M L Maodi, S T Rataemane, T Kyaw</p><p><strong>19. The identification of novel genes in anxiety disorders: A gene X environment correlation and interaction study</strong></p><p><strong></strong>N W McGregor, J Dimatelis, S M J Hemmings, C J Kinnear, D J Stein, V Russel, C Lochner</p><p><strong>20. Collaborations between conventional medicine and traditional healers: Obstacles and possibilities</strong></p><p><strong></strong>G Nortje, S Seedat, O Gureje</p><p><strong>21. Thought disorder and form perception: Relationships with symptoms and cognitive function in first-episode schizophrenia</strong></p><p>M R Olivier, R Emsley</p><p><strong>22. Investigating the functional significance of genome-wide variants associated with antipsychotic treatment response</strong></p><p><strong></strong>E Ovenden, B Drogemoller, L van der Merwe, R Emsley, L Warnich</p><p><strong>23. The moral and bioethical determinants of "futility" in psychiatry</strong></p><p><strong></strong>W P Pienaar</p><p><strong>24. Single voxel proton magnetic resonance spectroscopy (1H-MRS) and volumetry of the amylgdala in social anxiety disorder in the context of early developmental trauma</strong></p><p>D Rosenstein, A T Hess, J Zwart, F Ahmed-Leitao, E Meintjies, S Seedat</p><p><strong>25. Schizoaffective disorder in an acute psychiatric unit: Profile of users and agreement with Operational Criteria (OPCRIT)</strong></p><p><strong></strong>R R Singh, U Subramaney</p><p><strong>26. The right to privacy and confidentiality: The ethics of expert diagnosis in the public media and the Oscar Pistorius trial</strong></p><p><strong></strong>C Smith</p><p><strong>27. A birth cohort study in South Africa: A psychiatric perspective</strong></p><p>D J Stein</p><p><strong>28. 'Womb Raiders': Women referred for observation in terms of the Criminal Procedures Act (CPA) charged with fetal abduction and murder</strong></p><p><strong></strong>U Subramaney</p><p><strong>29. Psycho-pharmacology of sleep wake disorders: An update</strong></p><p>R Sykes</p><p><strong>30. Refugee post-settlement in South Africa: Role of adjustment challenges and family in mental health outcomes</strong></p><p><strong></strong>L Thela, A Tomita, V Maharaj, M Mhlongo, K Jonathan</p><p><strong>31. Dstinguishing ADHD symptoms in psychotic disorders: A new insight in the adult ADHD questionnaire</strong></p><p>Y van der Zee, M Borg, J H Hsieh, H Temmingh, D J Stein, F M Howells</p><p><strong>32. Oscar Pistorius ethical dilemmas in a trial by media: Does this include psychiatric evaluation by media?</strong></p><p>M Vorster</p><p><strong>33. Genetic investigation of apetite aggression in South African former young offenders: The involvement of serotonin transporter gene</strong></p><p>K Xulu, J Somer, M Hinsberger, R Weierstall, T Elbert, S Seedat, S Hemmings</p><p><strong>34. Effects of HIV and childhood trauma on brain morphemtry and neurocognitive function</strong></p><p>G Spies, F Ahmed-Leitao, C Fennema-Notestine, M Cherner, S Seedat</p><p><strong>35. Measuring intentional behaviour normative data of a newly developed motor task battery</strong></p><p><strong></strong>S Bakelaar, J Blampain, S Seedat, J van Hoof, Y Delevoye-Turrel</p><p><strong>36. Resilience in social anxiety disorder and post-traumatic stress disorder in the context of childhood trauma</strong></p><p>M Bship, S Bakelaar, D Rosenstein, S Seedat</p><p><strong>37. The ethical dilemma of seclusion practices in psychiatry</strong></p><p>G Chiba, U Subramaney</p><p><strong>38. Physical activity and neurological soft signs in patients with schizophrenia</strong></p><p>O Esan, C Osunbote, I Oladele, S Fakunle, C Ehindero</p><p><strong>39. A retrospective study of completed suicides in the Nelson Mandela Bay Metropolitan Area from 2008 to 2013 - preliminary results</strong></p><p><strong></strong>C Grobler, J Strumpher, R Jacobs</p><p><strong>40. Serotonin transporter variants play a role in anxiety sensitivity in South African adolescents</strong></p><p><strong></strong>S M J Hemmings, L I Martin, L van der Merwe, R Benecke, K Domschke, S Seedat</p><p><strong>41. Investigation of variants within antipsychotic candidate pharmacogenes associated with treatment outcome</strong></p><p>F Higgins, B Drogmoller, G Wright, L van der Merwe, N McGregor, B Chiliza, L Asmal, L Koen, D Niehaus, R Emsley, L Warnich</p><p><strong>42. Effects of diet, smoking and alcohol consumption on disability (EDSS) in people diagnosed with multiple sclerosis</strong></p><p>S Janse van Rensburg, W Davis, D Geiger, F J Cronje, L Whati, M Kidd, M J Kotze</p><p><strong>43. The clinical utility of neuroimaging in an acute adolescnet psychiatric inpatient population</strong></p><p><strong></strong>Z Khan, A Lachman, J Harvey</p><p><strong>44. Relationships between childhood trauma (CT) and premorbid adjustment (PA) in a highly traumatised sample of patients with first-episode schizophrenia (FES</strong>)</p><p>S Kilian, J Burns, S Seedat, L Asmal, B Chiliza, S du Plessis, R Olivier, R Emsley</p><p><strong>45. Functional and cognitive outcomes using an mTOR inhibitor in an adolescent with TSC</strong></p><p>A Lachman, C van der Merwe, P Boyes, P de Vries</p><p><strong>46. Perceptions about adolescent body image and eating behaviour</strong></p><p><strong></strong>K Laxton, A B R Janse van Rensburg</p><p><strong>47. Clinical relevance of FTO rs9939609 as a determinant of cardio-metabolic risk in South African patients with major depressive disorder</strong></p><p>H K Luckhoff, M J Kotze</p><p><strong>48. Childhood abuse and neglect as predictors of deficits in verbal auditory memory in non-clinical adolescents with low anxiety proneness</strong></p><p>L Martin, K Martin, S Seedat</p><p><strong>49. The changes of pro-inflammatory cytokines in a prenatally stressed febrile seizure animal model and whether <em>Rhus chirindensis</em> may attenuate these changes</strong></p><p><strong></strong>A Mohamed, M V Mabandla, L Qulu</p><p><strong>50. Influence of TMPRSS6 A736v and HFE C282y on serum iron parameters and age of onset in patients with multiple sclerosis</strong></p><p><strong></strong>K E Moremi, M J Kotze, H K Luckhoff, L R Fisher, M Kidd, R van Toorn, S Janse van Rensburg</p><p><strong>51. Polypharmacy in pregnant women with serious mental illness</strong></p><p>E Thomas, E du Toit, L Koen, D Niehaus</p><p><strong>52. Infant attachment and maternal depression as predictors of neurodevelopmental and behavioural outcomes at follow-up</strong></p><p>J Nothling, B Laughton, S Seedat</p><p><strong>53. Differences in abuse, neglect and exposure to community violence in adolescents with and without PTSD</strong></p><p><strong></strong>J Nothling, S Suliman, L Martin, C Simmons, S Seedat</p><p><strong>54. Assessment of oxidative stress markers in children with autistic spectrum disorders in Lagos, Nigeria</strong></p><p><strong></strong>Y Oshodi, O Ojewunmi, T A Oshodi, T Ijarogbe, O F Aina, J Okpuzor, O C F E A Lesi</p><p><strong>55. Change in diagnosis and management of 'gender identity disorder' in pre-adolescent children</strong></p><p>S Pickstone-Taylor</p><p><strong>56. Brain network connectivity in women exposed to intimate partner violence</strong></p><p>A Roos, J-P Fouche, B Vythilingum, D J Stein</p><p><strong>57. Prolonged exposure treatment for PTSD in a Third-World, task-shifting, community-based environment</strong></p><p>J Rossouw, E Yadin, I Mbanga, T Jacobs, W Rossouw, D Alexander, S Seedat</p><p><strong>58. Contrasting effects of early0life stress on mitochondrial energy-related proteins in striatum and hippocampus of a rat model of attention-deficit/ hyperactivity disorder</strong></p><p><strong></strong>V Russell, J Dimatelis, J Womersley, T-L Sterley</p><p><strong>59. Attention-deficit hyperactivity disorder in adults: A South African perspective</strong></p><p>R Schoeman, M de Klerk, M Kidd</p><p><strong>60. Cognitive function in women with HIV infection and early-life stress</strong></p><p>G Spies, C Fennema-Notestine, M Cherner, S Seedat</p><p><strong>61. Changes in functional connectivity networks in bipolar disorder patients after mindfulness-based cognitic therapy</strong></p><p>J A Starke, C F Beckmann, N Horn</p><p><strong>62. Post-traumatic stress disorder, overweight and obesity: A systematic review and meta-analysis</strong></p><p><strong></strong>S Suliman, L Anthonissen, J Carr, S du Plessis, R Emsley, S M J Hemmings, C Lochner, N McGregor L van den Heuvel, S Seedat</p><p><strong>63. The brain and behaviour in a third-trimester equivalent animal model of fetal alcohol spectrum disorders</strong></p><p>P C Swart, C B Currin, J J Dimatelis, V A Russell</p><p><strong>64. Irritability Assessment Model (IAM) to monitor irritability in child and adolescent psychiatric disorders.</strong></p><p>D van der Westhuizen</p><p><strong>65. Outcome of parent-adolescent training in chilhood victimisation: Adaptive functioning, psychosocial and physiological variables</strong></p><p>D van der Westhuizen</p><p><strong>66. The effect of ketamine in the Wistar-Kyoto and Sprague Dawley rat models of depression</strong></p><p>P J van Zyl, J J Dimatelis, V A Russell</p><p><strong>67. Investigating COMT variants in anxiety sensitivity in South African adolescents</strong></p><p>L J Zass, L Martin, S Seedat, S M J Hemmings</p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p><strong><br /></strong></p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p>