Bora-diaza-indacene based fluorescent probes for simultaneous visualisation of lipid droplets and endoplasmic reticulum.

Organelle selective fluorescent probes, especially those capable of concurrent detection of specific organelles, are of benefit to the research community in delineating the interplay between various organelles and the impact of such interaction in maintaining cellular homeostasis and its disruption in the diseased state. Although very useful, such probes are synthetically challenging to design due to the stringent lipophilicity requirement posed by different organelles, and hence, the lack of such probes being reported so far. This work details the synthesis, photophysical properties, and cellular imaging studies of two bora-diaza-indacene based fluorescent probes that can specifically and simultaneously visualise lipid droplets and endoplasmic reticulum; two organelles suggested having close interactions and implicated in stress-induced cellular dysfunction and disease progression.

BEERS2: RNA-Seq simulation through high fidelity in silico modeling.

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

A Novel Design-Thinking, Hospital Innovation Core Certificate Curriculum for Radiologists and Trainees: Creation, Implementation, and Multiyear Results.

RATIONALE AND OBJECTIVES: Innovation is a crucial skill for physicians and researchers, yet traditional medical education does not provide instruction or experience to cultivate an innovative mindset. This study evaluates the effectiveness of a novel course implemented in an academic radiology department training program over a 5-year period designed to educate future radiologists on the fundamentals of medical innovation. MATERIALS AND METHODS: A pre- and post-course survey and examination were administered to residents who participated in the innovation course (MESH Core) from 2018 to 2022. Respondents were first evaluated on their subjective comfort level, understanding, and beliefs on innovation-related topics using a 5-point Likert-scale survey. Respondents were also administered a 21-question multiple-choice exam to test their objective knowledge of innovation-related topics. RESULTS: Thirty-eight residents participated in the survey (response rate 95%). Resident understanding, comfort and belief regarding innovation-related topics improved significantly (P < .0001) on all nine Likert-scale questions after the course. After the course, a significant majority of residents either agreed or strongly agreed that technological innovation should be a core competency for the residency curriculum, and that a workshop to prototype their ideas would be beneficial. Performance on the course exam showed significant improvement (48% vs 86%, P < .0001). The overall course experience was rated 5 out of 5 by all participants. CONCLUSION: MESH Core demonstrates long-term success in educating future radiologists on the basic concepts of medical technological innovation. Years later, residents used the knowledge and experience gained from MESH Core to successfully pursue their own inventions and innovative projects. This innovation model may serve as an approach for other institutions to implement training in this domain.

Involvement of the tumour necrosis factor receptor system in glioblastoma cell death induced by palbociclib-heptamethine cyanine dye conjugate.

Glioblastoma is the most common and aggressive primary brain tumour in adults. The development of anti-brain cancer agents are challenged by the blood-brain barrier and the resistance conferred by the local tumour microenvironment. Heptamethine cyanine dyes (HMCDs) are a class of near-infrared fluorescence compounds that have recently emerged as promising agents for drug delivery. We conjugated palbociclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, to an HMCD, MHI-148, and conducted drug activity analysis on primary patient-derived glioblastoma cell lines. In addition to the expected cytostatic activity, our in vitro studies revealed that palbociclib-MHI-148 conjugate resulted in an almost 100-fold increase in cytotoxicity compared to palbociclib alone. This shift of palbociclib from cytostatic to cytotoxic when conjugated to MHI-148 was due to increased DNA damage, as indicated by an increase in γH2AX foci, followed by an increased expression of key extrinsic apoptosis genes, including TP53, TNFR1, TRAIL, FADD and caspase 8. In addition, we observed a time-dependent increase in the cell surface expression of TNFR1, consistent with an observed increase in the secretion TNFα, followed by TNFR1 endocytosis at 48 h. The treatment of patient GBM cells with the palbociclib-MHI-148 conjugate prevented TNFα-induced NFκB translocation, suggesting conjugate-induced TNFR1 signalling favoured the TNFR1-mediated apoptotic response rather than the pro-inflammatory response pathway. Notably, pharmacological inhibition of endocytosis of TNFR1, and siRNA-knockdown of TNFR1 reversed the palbociclib-MHI-148-induced cell death. These results show a novel susceptibility of glioblastoma cells to TNFR1-dependent apoptosis, dependent on inhibition of canonical NFκB signalling using our previously reported palbociclib-HMCD conjugate. Video Abstract.

BEERS2: RNA-Seq simulation through high fidelity in silico modeling.

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

ATG9 vesicles comprise the seed membrane of mammalian autophagosomes.

As the autophagosome forms, its membrane surface area expands rapidly, while its volume is kept low. Protein-mediated transfer of lipids from another organelle to the autophagosome likely drives this expansion, but as these lipids are only introduced into the cytoplasmic-facing leaflet of the organelle, full membrane growth also requires lipid scramblase activity. ATG9 harbors scramblase activity and is essential to autophagosome formation; however, whether ATG9 is integrated into mammalian autophagosomes remains unclear. Here we show that in the absence of lipid transport, ATG9 vesicles are already competent to collect proteins found on mature autophagosomes, including LC3-II. Further, we use styrene-maleic acid lipid particles to reveal the nanoscale organization of protein on LC3-II membranes; ATG9 and LC3-II are each fully integrated into expanding autophagosomes. The ratios of these two proteins at different stages of maturation demonstrate that ATG9 proteins are not continuously integrated, but rather are present on the seed vesicles only and become diluted in the expanding autophagosome membrane.

Perspectives of Dermatology Program Directors on the Impact of Step 1 Pass/Fail.

INTRODUCTION: The shift of Step 1 to Pass/Fail has generated several questions and concerns about obtaining residency positions among allopathic and osteopathic students alike. Determining the perspectives of Dermatology Program Directors in regards to post-Step 1 Pass/Fail is critical for students to better prepare for matching into dermatology. METHODS: After receiving Institutional Review Board (IRB) exemption status, the program directors were chosen from 144 Accreditation Council for Graduate Medical Education (ACGME) and 27 American Osteopathic Association (AOA) Dermatology programs using contact information from their respective online website databases. An eight-item survey was constructed on a three-point Likert scale, one free text response, and four demographic questions. The anonymous survey was sent out over the course of three weeks with weekly individualized reminder requests for participation. RESULTS: A total of 54.54% of responders had "Letters of Recommendation" in their top 3. Forty-five percent of responders had "Completed Audition Rotation at Program" in their top 3. And, 38.09% of responders had "USMLE Step 2 CK Scores" in their top 3. CONCLUSION: Approximately 50% of responders agreed that all medical students will have more difficulty matching dermatology. Based on the survey study, Dermatology program directors want to focus more on letters of recommendation, audition rotations, and Step 2 CK scores. Because each field seems to prioritize different aspects of an application, students should attempt to gain as much exposure to different fields such as through research and shadowing to narrow down their ideal specialties. Consequently, the student will have more time to tailor their applications to what residency admissions are looking for.

Measurement of Complement Activation via Plasma-Soluble C5b-9 Comparison with Terminal Complement Complex Staining in a Series of Kidney Biopsies.

INTRODUCTION: With the emergence of therapeutic complement inhibitors, there is a need to identify patients with complement-driven inflammation. C5b-9 is the terminal product of the three complement pathways and therefore a marker of total complement activation. We present a pilot study which aims to assess whether plasma soluble C5b-9 (sC5b-9) correlates with terminal complement complex (TCC) staining in kidney tissue. The secondary aim was to assess the utility of plasma sC5b-9 as part of routine workup in kidney patients undergoing kidney biopsy. METHODS: Thirty-seven patients undergoing kidney biopsy had plasma sC5b-9 and TCC staining on kidney tissue performed. Additional blood markers including creatinine, haemoglobin, CRP, factor H, factor I, and midkine levels were also taken. These parameters were correlated with the histological diagnoses. Patients were divided into a diseased group (n = 31) and a control group (n = 6) consisting of transplanted kidneys with minor or no changes. Of the biopsies in the control group, 50% were performed as per protocol, and the other 50% were performed due to clinical need. RESULTS: There was no correlation found between plasma sC5b-9 and TCC kidney staining. Elevated sC5b-9 levels were found in a heterogeneous group of patients but were associated with higher CRP and lower haemoglobin levels. Overall, there was more TCC kidney staining in the diseased group compared with the control group, and a trend was observed of diabetic, primary membranous nephropathy, and amyloidosis patients having more intense glomerular and peritubular/interstitial staining. CONCLUSION: Plasma sC5b-9 as a marker of total complement activation does not correlate with TCC kidney staining. This discordance suggests that plasma sC5b-9 and TCC staining are distinct markers of disease. TCC staining reflects chronicity and tissue deposition of complement over time. Conversely, plasma sC5b-9 concentrations change rapidly and reflect systemic complement activation. Complement activation was present in a heterogeneous group of kidney disease, indicating the underlying role of complement in many disorders.

Elucidating the cellular uptake mechanisms of heptamethine cyanine dye analogues for their use as an anticancer drug-carrier molecule for the treatment of glioblastoma.

The development of chemotherapies for glioblastoma is hindered by their limited bioavailability and toxicity on normal brain function. To overcome these limitations, we investigated the structure-dependent activity of heptamethine cyanine dyes (HMCD), a group of tumour-specific and BBB permeable near-infrared fluorescent dyes, in both commercial (U87MG) and patient-derived GBM cell lines. HMCD analogues with strongly ionisable sulphonic acid groups were not taken up by patient-derived GBM cells, but were taken up by the U87MG cell line. HMCD uptake relies on a combination of transporter uptake through organic anion-transporting polypeptides (OATPs) and endocytosis into GBM cells. The uptake of HMCDs was not affected by p-glycoprotein efflux in GBM cells. Finally, we demonstrate structure-dependent cytotoxic activity at high concentrations (EC50 : 1-100 µM), likely due to mitochondrial damage-induced apoptosis. An in vivo orthotopic glioblastoma model highlights tumour-specific accumulation of our lead HMCD, MHI-148, for up to 7 days following a single intraperitoneal injection. These studies suggest that strongly ionisable groups like sulphonic acids hamper the cellular uptake of HMCDs in patient-derived GBM cell lines, highlighting cell line-specific differences in HMCD uptake. We envisage these findings will help in the design and structural modifications of HMCDs for drug-delivery applications for glioblastoma.

Single-cell image analysis reveals over-expression of organic anion transporting polypeptides (OATPs) in human glioblastoma tissue.

Background: Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults. Whilst the role of the efflux transporters are well established in GBM, the expression and function of uptake transporters, such as the organic anion transporting polypeptide (OATP) family, are not well understood. OATPs possess broad substrate specificity that includes anti-cancer agents; therefore, we sought to investigate the expression of four OATP isoforms in human GBM cell types using patient tumor tissue. Methods: We used fluorescent immunohistochemical labeling of paraffin-embedded surgically resected tissues and single-cell image analysis methods to explore the expression of the OATP isoforms in different tumor cell types through co-labeling with cell-type specific markers, such as IBA1 (pan-myeloid), GFAP (tumor cell), PDGFRß (stromal cell), and UEA-1-lectin (endothelial). Results: We found significant over-expression of all the OATP isoforms (OATP1A2, 2B1, 1C1 and 4A1) in GBM tumor sections when compared to non-neoplastic brain. A single-cell image analysis revealed that OATPs were significantly upregulated throughout the tumor parenchyma, with significantly higher expression found on lectin-positive blood vessels and IBA1-positive myeloid cells in GBM compared to non-tumor brain tissue. Qualitative analysis of the four OATP isoforms demonstrated greater expression of OATP4A1 in peri-necrotic regions of GBM tissue, which correlated with hypoxia-related markers within the Ivy GAP RNAseq dataset. Conclusion: Here, we demonstrate, for the first time, the protein expression of four OATPs in human GBM tissue, including upregulation within the tumor microenvironment by myeloid cells and tumor vasculature, and isoform-specific upregulation within hypoxic niches.

Synthesis and Structure-Activity Relationships for the Anti-Mycobacterial Activity of 3-Phenyl-N-(Pyridin-2-ylmethyl)Pyrazolo[1,5-a]Pyrimidin-7-Amines.

Pyrazolo[1,5-a]pyrimidines have been reported as potent inhibitors of mycobacterial ATP synthase for the treatment of Mycobacterium tuberculosis (M.tb). In this work, we report the design and synthesis of approximately 70 novel 3,5-diphenyl-N-(pyridin-2-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amines and their comprehensive structure-activity relationship studies. The most effective pyrazolo[1,5-a]pyrimidin-7-amine analogues contained a 3-(4-fluoro)phenyl group, together with a variety of 5-alkyl, 5-aryl and 5-heteroaryl substituents. A range of substituted 7-(2-pyridylmethylamine) derivatives were also active. Some of these compounds exhibited potent in vitro M.tb growth inhibition, low hERG liability and good mouse/human liver microsomal stabilities, highlighting their potential as inhibitors of M.tb.

Acute kidney injury development in polytrauma and the safety of early repeated contrast studies: A retrospective cohort study.

BACKGROUND: The role of repeat intravenous contrast doses beyond initial contrast imaging in the development of acute kidney injury (AKI) for multiple injury patients admitted to the intensive care unit (ICU) is not fully understood. We hypothesized that additional contrast doses are potentially modifiable risk factors for worse outcomes. METHODS: An 8-year retrospective study of our institutional prospective postinjury multiple organ failure database was performed. Adult ICU admissions that survived >72 hours with Injury Severity Score (ISS) of >15 were included. Patients were grouped based on number of repeat contrast studies received after initial imaging. Initial vital signs, resuscitation data, and laboratory parameters were collected. Primary outcome was AKI (Kidney Disease: Improving Global Outcomes criteria), and secondary outcomes included contrast-induced acute kidney injury (CI-AKI; >25% or >44 µmol/L increase in creatinine within 72 hours of contrast administration), multiple organ failure, length of stay, and mortality. RESULTS: Six-hundred sixty-three multiple injury patients (age, 45.3 years [SD, 9.1 years]; males, 75%; ISS, 25 (interquartile range, 20-34); mortality, 5.4%) met the inclusion criteria. The incidence of AKI was 13.4%, and CI-AKI was 14.5%. Multivariate analysis revealed that receiving additional contrast doses within the first 72 hours was not associated with AKI (odds ratio, 1.33; confidence interval, 0.80-2.21; p = 0.273). Risk factors for AKI included higher ISS ( p < 0.0007), older age ( p = 0.0109), higher heart rate ( p = 0.0327), lower systolic blood pressure ( p = 0.0007), and deranged baseline blood results including base deficit ( p = 0.0042), creatinine ( p < 0.0001), lactate ( p < 0.0001), and hemoglobin ( p = 0.0085). Acute kidney injury was associated with worse outcomes (ICU length of stay: 8 vs. 3 days, p < 0.0001; mortality: 16% vs. 3.8%, p < 0.0001; MOF: 42% vs. 6.6%, p < 0.0001). CONCLUSION: There is a limited role of repeat contrast administration in AKI development in ICU-admitted multiple injury patients. The clinical significance of CI-AKI is likely overestimated, and it should not compromise essential secondary imaging from the ICU. Further prospective studies are needed to verify our results. LEVEL OF EVIDENCE: Therapeutic/Care Management; Level III.

Synthetic studies towards isomeric pyrazolopyrimidines as potential ATP synthesis inhibitors of Mycobacterium tuberculosis. Structural correction of reported N-(6-(2-(dimethylamino)ethoxy)-5-fluoropyridin-3-yl)-2-(4-fluorophenyl)-5-(trifluoromethyl)pyrazolo[1,5-α]pyrimidin-7-amine.

During our studies into preparing analogues of pyrazolopyrimidine as ATP synthesis inhibitors of Mycobacterium tuberculosis, a regiospecific condensation reaction between ethyl 4,4,4-trifluoroacetoacetate and 3-(4-fluorophenyl)-1H-pyrazol-5-amine was observed which was dependent on the specific reaction conditions employed. This work identifies optimized reaction conditions to access either the pyrazolo[3,4-ß]pyridine or the pyrazolo[1,5-α]pyrimidine scaffold. This has led to the structural confirmation of the previously reported pyrazolopyrimidine 17b which was reported as pyrazolo[1,5-α]pyrimidine structure 2 which was corrected to pyrazolo[3,4-ß]-pyrimidine 19.

A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer.

Androgen receptor (AR) signaling is the central driver of prostate cancer across disease states. While androgen deprivation therapy (ADT) is effective in the initial treatment of prostate cancer, resistance to ADT or to next-generation androgen pathway inhibitors invariably arises, most commonly through the re-activation of the AR axis. Thus, orthogonal approaches to inhibit AR signaling in advanced prostate cancer are essential. Here, via genome-scale CRISPR-Cas9 screening, we identify protein arginine methyltransferase 1 (PRMT1) as a critical mediator of AR expression and signaling. PRMT1 regulates the recruitment of AR to genomic target sites and the inhibition of PRMT1 impairs AR binding at lineage-specific enhancers, leading to decreased expression of key oncogenes, including AR itself. In addition, AR-driven prostate cancer cells are uniquely susceptible to combined AR and PRMT1 inhibition. Our findings implicate PRMT1 as a key regulator of AR output and provide a preclinical framework for co-targeting of AR and PRMT1 in advanced prostate cancer.

Conjugation of Palbociclib with MHI-148 Has an Increased Cytotoxic Effect for Breast Cancer Cells and an Altered Mechanism of Action.

The CDK4/6 inhibitor palbociclib, combined with endocrine therapy, has been shown to be effective in postmenopausal women with estrogen receptor-positive, HER2-negative advanced or metastatic breast cancer. However, palbociclib is not as effective in the highly aggressive, triple-negative breast cancer that lacks sensitivity to chemotherapy or endocrine therapy. We hypothesized that conjugation of the near-infrared dye MHI-148 with palbociclib can produce a potential theranostic in triple-negative, as well as estrogen receptor-positive, breast cancer cells. In our study, the conjugate was found to have enhanced activity in all mammalian cell lines tested in vitro. However, the conjugate was cytotoxic and did not induce G1 cell cycle arrest in breast cancer cells, suggesting its mechanism of action differs from the parent compound palbociclib. The study highlights the importance of investigating the mechanism of conjugates of near-infrared dyes to therapeutic compounds, as conjugation can potentially result in a change of mechanism or target, with an enhanced cytotoxic effect in this case.

Synthesis and structure-activity relationships for a new class of tetrahydronaphthalene amide inhibitors of Mycobacterium tuberculosis.

Drug resistant tuberculsosis (TB) is global health crisis that demands novel treatment strategies. Bacterial ATP synthase inhibitors such as bedaquiline and next-generation analogues (such as TBAJ-876) have shown promising efficacy in patient populations and preclinical studies, respectively, suggesting that selective targeting of this enzyme presents a validated therapeutic strategy for the treatment of TB. In this work, we report tetrahydronaphthalene amides (THNAs) as a new class of ATP synthase inhibitors that are effective in preventing the growth of Mycobacterium tuberculosis (M.tb) in culture. Design, synthesis and comprehensive structure-activity relationship studies for approximately 80 THNA analogues are described, with a small selection of compounds exhibiting potent (in some cases MIC90 <1 µg/mL) in vitro M.tb growth inhibition taken forward to pharmacokinetic and off-target profiling studies. Ultimately, we show that some of these THNAs possess reduced lipophilic properties, decreased hERG liability, faster mouse/human liver microsomal clearance rates and shorter plasma half-lives compared with bedaquiline, potentially addressing of the main concerns of persistence and phospholipidosis associated with bedaquiline.

Proximal humeral fracture-dislocations: which patterns can be reduced in the emergency department?

BACKGROUND: Shoulder fracture-dislocations can represent a challenging management scenario in the emergency department (ED) because of concern for the presence of occult fractures that may displace during a reduction attempt. The alternative, a closed reduction attempt in the operating room, has the benefit of full paralysis but requires additional resource utilization. There is limited guidance in the literature about the risks of an initial reduction attempt in the ED as a function of fracture pattern to help guide physicians with this decision. METHODS: This was a retrospective case review of adult patients with shoulder dislocations and fracture-dislocations seen in the ED at a level 1 trauma center over a 10-year period. Imaging and medical records were reviewed to evaluate whether the reduction attempt was successful, unsuccessful without worsening, or unsuccessful with worsening alignment of any fractures, as well as the ultimate clinical outcome. RESULTS: We identified 165 patients with fracture-dislocations and 484 patients with simple dislocations during the same period. Of the patients with fracture-dislocations, 103 had greater tuberosity fractures, 12 had nondisplaced surgical neck fractures, and 50 had displaced surgical neck fractures. None of the patients with simple dislocations had displacement during an ED reduction attempt, including 100 patients aged >65 years. Of the 103 patients with greater tuberosity fracture-dislocations, only 1 had displacement of a humeral shaft fracture during ED reduction. Displacement occurred in 6 of 8 patients with nondisplaced neck fractures who underwent an initial ED reduction attempt vs. 1 of 4 patients who underwent the initial reduction attempt in the operating room. ED reduction was attempted in 25 of the 50 displaced humeral neck fracture-dislocations and was successful in 10 of these (40%). CONCLUSIONS: For patients with greater tuberosity fracture-dislocations, there is a low rate of displacement with a reduction attempt in the ED, but an ED reduction attempt in nondisplaced neck fractures is not recommended because of the high rate of displacement. For displaced neck fractures, closed reduction can be successful in select patients. Finally, these data confirm prior reports that closed reduction of simple shoulder dislocations in patients aged >65 years is safe in the ED.

A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.

Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3' noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.