Publications by authors named "Kevin P White"

212 Publications

Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in .

Genes (Basel) 2021 12 26;13(1). Epub 2021 Dec 26.

Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA.

Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in , that unexpectedly diverged rapidly from its parent, , an extremely conserved component in the CCR4-NOT machinery in post-transcriptional and post-translational regulation of eukaryotic cells, and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the   genome. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing ChIP-Seq data from and to the ancestral Caf40 binding events from , a species that diverged before the duplication event, we found a dynamic pattern in which Zeus binding rapidly coevolved with a previously unknown DNA motif, which we term Caf40 and Zeus-Associated Motif (CAZAM), under the influence of positive selection. Interestingly, while both copies of acquired targets at male-biased and testis-specific genes, and proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Using CRISPR-Cas9-mediated gene knockout of and RNA-Seq, we found that regulated the expression of 661 differentially expressed genes (DEGs). Our results suggest that the evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic genome-wide evolutionary processes associated with new genes.
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http://dx.doi.org/10.3390/genes13010057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8774992PMC
December 2021

Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes.

Nat Commun 2021 11 26;12(1):6946. Epub 2021 Nov 26.

Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.

Black women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast cancers, with RNA-seq in a subset, from women in Nigeria in comparison with The Cancer Genome Atlas (n = 76) reveal a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonal GATA3 mutations with a 10.5-year younger age at diagnosis. We also find non-coding mutations in bona fide drivers (ZNF217 and SYPL1) and a previously unreported INDEL signature strongly associated with African ancestry proportion, underscoring the need to expand inclusion of diverse populations in biomedical research. Finally, we demonstrate that characterizing tumors for homologous recombination deficiency has significant clinical relevance in stratifying patients for potentially life-saving therapies.
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http://dx.doi.org/10.1038/s41467-021-27079-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626467PMC
November 2021

The role of Cushing's reflex and the vasopressin-mediated oligoanuric response to intracranial hypertension in patients with abdominal compartment syndrome.

Surgery 2022 02 24;171(2):399-404. Epub 2021 Oct 24.

Section of Minimally Invasive Surgery, Department of General Surgery, Cleveland Clinic Florida, Weston, FL. Electronic address:

Background: We examined the link between increased intra-abdominal pressure, intracranial pressure, and vasopressin release as a potential mechanism. Intra-abdominal pressure, produced by abdominal-cavity insufflation with carbon dioxide (CO) during laparoscopic abdominal procedures to facilitate visualization, is associated with various complications, including arterial hypertension and oliguria.

Methods: Mean arterial pressure, optic nerve sheath diameter, measured as a proxy for intracranial pressure, plasma vasopressin, serum and urine osmolarity, and urine output were measured 4 times during laparoscopic sleeve gastrectomy in 42 patients: before insufflation with CO (T); after insufflation to 15 cm water (HO) pressure, with 5 cm HO positive end-expiratory pressure (T); after positive end-expiratory pressure was raised to 10 cm HO (T); and after a return to the baseline state (T). Mean values at T to T and the directional consistency of changes (increase/decrease/ unchanged) were compared among the 4 data-collection points.

Results: Statistically significant elevations (all P ≤ .001) were noted from T to T and from T to T in mean arterial pressure, optic nerve sheath diameter, and vasopressin, followed by decreases at T. For optic nerve sheath diameter and vasopressin, the increases at T and T occurred in 98% and 100% of patients, ultimately exceeding normal levels in 88 and 97%, respectively. Conversely, urine output fell from T to T and T by 60.9 and 73.4%, decreasing in 88.1% of patients (all P < .001). Patients with class II obesity exhibited statistically greater increases in optic nerve sheath diameter and vasopressin, but statistically less impact on urine output, than patients with class III obesity.

Conclusion: Increased mean arterial pressure, intracranial pressure, and vasopressin release appear to be intermediary steps between increased intra-abdominal pressure and oliguria. Further research is necessary to determine any causative links between these physiological changes.
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http://dx.doi.org/10.1016/j.surg.2021.08.046DOI Listing
February 2022

Nerve autofluorescence under near-ultraviolet light: cutting-edge technology for intra-operative neural tissue visualization in 17 patients.

Surg Endosc 2022 Jun 25;36(6):4079-4089. Epub 2021 Oct 25.

Florida Department of General Surgery, Cleveland Clnic Florida, 2950 Cleveland Clinic Boulevard, Weston, FL, 33331, USA.

Background: Nerve visualization and the identification of other neural tissues during surgery is crucial for numerous reasons, including the prevention of iatrogenic nerve and neural structure injury and facilitation of nerve repair. However, current methods of intra-operative nerve detection are generally expensive, unproven, and/or technically challenging. Recently, we have documented, in both in vivo animal models and ex vivo human tissue, that nerves autofluorescence when viewed in near-ultraviolet light (NUV). In this paper, we describe our use of nerve autofluorescence to facilitate the visualization of nerves and other neural tissues intra-operatively in 17 patients undergoing a range of surgical procedures.

Methods: Employing the same prototype axon imaging system previously documented to markedly enhance nerve visualization in both in vivo animal and ex vivo human models, surgical fields were observed in 17 patients under both white and NUV light during parotid tumor resection (n = 3), thyroid tumor resection (n = 7), and surgery for peripheral nerve and spinal tumors and injury (n = 7).

Results: In all 17 patients, the intra-operative use of the imaging system both was feasible and markedly enhanced the localization of all neural tissues throughout their course within the surgical field. All 17 procedures were successful and devoid of any peri-operative complications or post-operative neurological deficits.

Conclusions: Intra-operatively visualizing auto-fluorescent peripheral nerves and other neural tissues under NUV light is feasible in human patients across a range of clinical scenarios and appears to appreciably enhance nerve and other neural tissue visualization. Controlled studies to explore this technology further are needed.
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http://dx.doi.org/10.1007/s00464-021-08729-yDOI Listing
June 2022

Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer.

Genome Med 2021 10 11;13(1):158. Epub 2021 Oct 11.

Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore.

Background: Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity-however, most predicted enhancer regions remain to be functionally tested.

Methods: We analyzed 132 epigenomic histone modification profiles of 18 primary gastric cancer (GC) samples, 18 normal gastric tissues, and 28 GC cell lines using Nano-ChIP-seq technology. We applied Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to assess functional enhancer activity. An Activity-by-contact (ABC) model was employed to explore the effects of histone acetylation and CapSTARR-seq levels on enhancer-promoter interactions.

Results: We report a comprehensive catalog of 75,730 recurrent predicted enhancers, the majority of which are GC-associated in vivo (> 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying CapSTARR-seq to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers, even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. We identified cancer-relevant genes (ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4α as a master trans-acting factor associated with GC enhancer heterogeneity.

Conclusions: Our results indicate that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, providing insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity.
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http://dx.doi.org/10.1186/s13073-021-00970-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8504099PMC
October 2021

Cluster of Pruritic Papules Refractory to Numerous Treatments: Challenge.

Am J Dermatopathol 2021 Oct;43(10):e116

Department of Dermatology, Oregon Health and Science University, Portland, OR.

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http://dx.doi.org/10.1097/DAD.0000000000001905DOI Listing
October 2021

Cluster of Pruritic Papules Refractory to Numerous Treatments: Answer.

Am J Dermatopathol 2021 Oct;43(10):753

Department of Dermatology, Oregon Health and Science University, Portland, OR.

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http://dx.doi.org/10.1097/DAD.0000000000001904DOI Listing
October 2021

A pan-cancer organoid platform for precision medicine.

Cell Rep 2021 07;36(4):109429

Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.

Patient-derived tumor organoids (TOs) are emerging as high-fidelity models to study cancer biology and develop novel precision medicine therapeutics. However, utilizing TOs for systems-biology-based approaches has been limited by a lack of scalable and reproducible methods to develop and profile these models. We describe a robust pan-cancer TO platform with chemically defined media optimized on cultures acquired from over 1,000 patients. Crucially, we demonstrate tumor genetic and transcriptomic concordance utilizing this approach and further optimize defined minimal media for organoid initiation and propagation. Additionally, we demonstrate a neural-network-based high-throughput approach for label-free, light-microscopy-based drug assays capable of predicting patient-specific heterogeneity in drug responses with applicability across solid cancers. The pan-cancer platform, molecular data, and neural-network-based drug assay serve as resources to accelerate the broad implementation of organoid models in precision medicine research and personalized therapeutic profiling programs.
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http://dx.doi.org/10.1016/j.celrep.2021.109429DOI Listing
July 2021

Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA.

NPJ Precis Oncol 2021 Jul 2;5(1):63. Epub 2021 Jul 2.

Tempus Labs, Chicago, IL, USA.

Liquid biopsy is a valuable precision oncology tool that is increasingly used as a non-invasive approach to identify biomarkers, detect resistance mutations, monitor disease burden, and identify early recurrence. The Tempus xF liquid biopsy assay is a 105-gene, hybrid-capture, next-generation sequencing (NGS) assay that detects single-nucleotide variants, insertions/deletions, copy number variants, and chromosomal rearrangements. Here, we present extensive validation studies of the xF assay using reference standards, cell lines, and patient samples that establish high sensitivity, specificity, and accuracy in variant detection. The Tempus xF assay is highly concordant with orthogonal methods, including ddPCR, tumor tissue-based NGS assays, and another commercial plasma-based NGS assay. Using matched samples, we developed a dynamic filtering method to account for germline mutations and clonal hematopoiesis, while significantly decreasing the number of false-positive variants reported. Additionally, we calculated accurate circulating tumor fraction estimates (ctFEs) using the Off-Target Tumor Estimation Routine (OTTER) algorithm for targeted-panel sequencing. In a cohort of 1,000 randomly selected cancer patients who underwent xF testing, we found that ctFEs correlated with disease burden and clinical outcomes. These results highlight the potential of serial testing to monitor treatment efficacy and disease course, providing strong support for incorporating liquid biopsy in the management of patients with advanced disease.
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http://dx.doi.org/10.1038/s41698-021-00202-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8253837PMC
July 2021

Corrugated Purple Plaque on the Left Cheek: Answer.

Am J Dermatopathol 2021 May;43(5):386-387

Department of Dermatology, Oregon Health & Science University, Portland, OR.

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http://dx.doi.org/10.1097/DAD.0000000000001682DOI Listing
May 2021

Accuracy and reliability of the AO Spine subaxial cervical spine classification system grading subaxial cervical facet injury morphology.

Eur Spine J 2021 06 11;30(6):1607-1614. Epub 2021 Apr 11.

Department of Orthopedic and Traumatology, Hospital Churruca Visca, Buenos Aires, Argentina.

Purpose: A classification system was recently developed by the international association AO Spine for assessing subaxial cervical spine fractures. Significant variability exists between users of the facet component, which consists of four morphological types (F1-F4). The primary aims of this study were to assess the diagnostic accuracy and reliability of this new system's facet injury morphological classifications.

Methods: A survey consisting of 16 computed tomography (CT) scans of patients with cervical facet fractures was distributed to spine surgeon members of AO Spine Latin America. To provide a gold standard diagnosis for comparison, all 16 injuries had been classified previously by six co-authors and only were included after total consensus was achieved. Demographic and surgical practice characteristics of all respondents were analyzed, and diagnostic accuracy calculated. Inter- and intra-observer agreement rates were calculated across two survey rounds, conducted one month apart.

Results: A total of 135 surgeons completed both surveys, among whom the mean age was 41.6 years (range 26-71), 130 (96.3%) were men, and 83 (61.5%) were orthopedic surgeons. The mean time in practice as a spine surgeon was 9.7 years (1-30). The overall diagnostic accuracy of all responses was 65.4%. Inter-observer and intra-observer agreement rates for F1/F2/F3/F4 were 55.4%/47.6%/64.0%/94.7% and 60.0%/49.1%/58.0%/93.0%, respectively.

Conclusion: This study evaluates the AO Spine Classification System specifically for facet injuries involving the subaxial cervical spine in a large sample of spine surgeons. There was significant variability in diagnostic accuracy for F1 through F3-type fractures, whereas almost universal agreement was achieved for F4-type injuries.
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http://dx.doi.org/10.1007/s00586-021-06837-wDOI Listing
June 2021

Nerve autofluorescence in near-ultraviolet light markedly enhances nerve visualization in vivo.

Surg Endosc 2022 03 9;36(3):1999-2005. Epub 2021 Apr 9.

Cleveland Clinic Florida, Weston, FL, 33325, USA.

Background: During surgery, surgeons must accurately localize nerves to avoid injuring them. Recently, we have discovered that nerves fluoresce in near-ultraviolet light (NUV) light. The aims of the current study were to determine the extent to which nerves fluoresce more brightly than background and vascular structures in NUV light, and identify the NUV intensity at which nerves are most distinguishable from other tissues.

Methods: We exposed sciatic nerves within the posterior thigh in five 250-300 gm Wistar rats, then observed them at four different NUV intensity levels: 20%, 35%, 50%, and 100%. Brightness of fluorescence was measured by fluorescence spectroscopy, quantified as a fluorescence score using Image-J software, and statistically compared between nerves, background, and both an artery and vein by unpaired Student's t tests with Bonferroni adjustment to accommodate multiple comparisons. Sensitivity, specificity, and accuracy were calculated for each NUV intensity.

Results: At 20, 35, 50, and 100% NUV intensity, fluorescence scores for nerves versus background tissues were 117.4 versus 40.0, 225.8 versus 88.0, 250.6 versus 121.4, and 252.8 versus 169.4, respectively (all p < 0.001). Fluorescence scores plateaued at 50% NUV intensity for nerves, but continued to rise for background. At 35%, 50%, and 100% NUV intensity, a fluorescence score of 200 was 100% sensitive, specific, and accurate identifying nerves. At 100 NUV intensity, artery and vein scores were 61.8 and 60.0, both dramatically lower than for nerves (p < 0.001).

Conclusions: At all NUV intensities ≥ 35%, a fluorescence score of 200 is 100% accurate distinguishing nerves from other anatomical structures in vivo.
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http://dx.doi.org/10.1007/s00464-021-08484-0DOI Listing
March 2022

Nerve spectroscopy: understanding peripheral nerve autofluorescence through photodynamics.

Surg Endosc 2021 12 29;35(12):7104-7111. Epub 2021 Mar 29.

Department of General Surgery & The Bariatric and Metabolic Institute, Cleveland Clinic Florida, 2950 Cleveland. Clinic Blvd, Weston, FL, 33331, USA.

Background: Being able to accurately identify sensory and motor nerves is crucial during surgical procedures to prevent nerve injury. We aimed to (1) evaluate the feasibility of performing peripheral human nerve visualization utilizing nerves' own autofluorescence in an ex-vivo model; (2) compare the effect of three different nerve fiber fixation methods on the intensity of fluorescence, indicated as the intensity ratio; and (3) similarly compare three different excitation ranges.

Methods: Samples from various human peripheral nerves were selected postoperatively. Nerve fibers were divided into three groups: Group A nerve fibers were washed with a physiologic solution; Group B nerve fibers were fixated with formaldehyde for 6 h first, and then washed with a physiologic solution; Group C nerve fibers were fixated with formaldehyde for six hours, but not washed afterwards. An Olympus IX83 inverted microscope was used for close-up image evaluation. Nerve fibers were exposed to white-light wavelength spectrums for a specific time frame prior to visualization under three different filters-Filter 1-LF405-B-OMF Semrock; Filter 2-U-MGFP; Filter 3-U-MRFPHQ Olympus, with excitation ranges of 390-440, 460-480, and 535-555, respectively. The fluorescence intensity of all images was subsequently analyzed using Image-J Software, and results compared by analysis of variance (ANOVA).

Results: The intensity ratios observed with Filter 1 failed to distinguish the different nerve fiber groups (p = 0.39). Conversely, the intensity ratios seen under Filters 2 and 3 varied significantly between the three nerve-fiber groups (p = 0.021, p = 0.030, respectively). The overall intensity of measurements was greater with Filter 1 than Filter 3 (p < 0.05); however, all nerves were well visualized by all filters.

Conclusion: The current results on ex vivo peripheral nerve fiber autofluorescence suggest that peripheral nerve fiber autofluorescence intensity does not greatly depend upon the excitation wavelength or fixation methods used in an ex vivo setting. Implications for future nerve-sparing surgery are discussed.
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http://dx.doi.org/10.1007/s00464-020-08227-7DOI Listing
December 2021

New regulators of Drosophila eye development identified from temporal transcriptome changes.

Genetics 2021 04;217(4)

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
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http://dx.doi.org/10.1093/genetics/iyab007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049564PMC
April 2021

Does near-infrared fluorescent cholangiography with indocyanine green reduce bile duct injuries and conversions to open surgery during laparoscopic or robotic cholecystectomy? - A meta-analysis.

Surgery 2021 Apr 18;169(4):859-867. Epub 2021 Jan 18.

Department of General Surgery, Cleveland Clinic Florida, Weston, FL. Electronic address:

Background: Bile duct injury and conversion-to-open-surgery rates remain unacceptably high during laparoscopic and robotic cholecystectomy. In a recently published randomized clinical trial, using near-infrared fluorescent cholangiography with indocyanine green intraoperatively markedly enhanced biliary-structure visualization. Our systematic literature review compares bile duct injury and conversion-to-open-surgery rates in patients undergoing laparoscopic or robotic cholecystectomy with versus without near-infrared fluorescent cholangiography.

Methods: A thorough PubMed search was conducted to identify randomized clinical trials and nonrandomized clinical trials with ≥100 patients. Because all near-infrared fluorescent cholangiography studies were published since 2013, only studies without near-infrared fluorescent cholangiography published since 2013 were included for comparison. Incidence estimates, weighted and unweighted for study size, were adjusted for acute versus chronic cholecystitis, and for robotic versus laparoscopic cholecystectomy and are reported as events/10,000 patients. All studies were assessed for bias risk and high-risk studies excluded.

Results: In total, 4,990 abstracts were reviewed, identifying 5 near-infrared fluorescent cholangiography studies (3 laparoscopic cholecystectomy/2 robotic cholecystectomy; n = 1,603) and 11 not near-infrared fluorescent cholangiography studies (5 laparoscopic cholecystectomy/4 robotic cholecystectomy/2 both; n = 5,070) for analysis. Overall weighted rates for bile duct injury and conversion were 6 and 16/10,000 in near-infrared fluorescent cholangiography patients versus 25 and 271/10,000 in patients without near-infrared fluorescent cholangiography. Among patients undergoing laparoscopic cholecystectomy, bile duct injuries, and conversion rates among near-infrared fluorescent cholangiography versus patients without near-infrared fluorescent cholangiography were 0 and 23/10,000 versus 32 and 255/10,000, respectively. Bile duct injury rates were low with robotic cholecystectomy with and without near-infrared fluorescent cholangiography (12 and 8/10,000), but there was a marked reduction in conversions with near-infrared fluorescent cholangiography (12 vs 322/10,000).

Conclusion: Although large comparative trials remain necessary, preliminary analysis suggests that using near-infrared fluorescent cholangiography with indocyanine green intraoperatively sizably decreases bile duct injury and conversion-to-open-surgery rates relative to cholecystectomy under white light alone.
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http://dx.doi.org/10.1016/j.surg.2020.12.008DOI Listing
April 2021

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq.

Nucleic Acids Res 2021 02;49(3):e17

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Chromatin immunoprecipitation (IP) followed by sequencing (ChIP-seq) is the gold standard to detect transcription-factor (TF) binding sites in the genome. Its success depends on appropriate controls removing systematic biases. The predominantly used controls, i.e. DNA input, correct for uneven sonication, but not for nonspecific interactions of the IP antibody. Another type of controls, 'mock' IP, corrects for both of the issues, but is not widely used because it is considered susceptible to technical noise. The tradeoff between the two control types has not been investigated systematically. Therefore, we generated comparable DNA input and mock IP experiments. Because mock IPs contain only nonspecific interactions, the sites predicted from them using DNA input indicate the spurious-site abundance. This abundance is highly correlated with the 'genomic activity' (e.g. chromatin openness). In particular, compared to cell lines, complex samples such as whole organisms have more spurious sites-probably because they contain multiple cell types, resulting in more expressed genes and more open chromatin. Consequently, DNA input and mock IP controls performed similarly for cell lines, whereas for complex samples, mock IP substantially reduced the number of spurious sites. However, DNA input is still informative; thus, we developed a simple framework integrating both controls, improving binding site detection.
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http://dx.doi.org/10.1093/nar/gkaa1155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7897498PMC
February 2021

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.

Genome Biol 2020 12 8;21(1):298. Epub 2020 Dec 8.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content. Furthermore, STARR-seq readout is confounded by RNA secondary structure and thermodynamic stability. To address these potential confounders, we developed a negative binomial regression framework for uniformly processing STARR-seq data, called STARRPeaker. Moreover, to aid our effort, we generated whole-genome STARR-seq data from the HepG2 and K562 human cell lines and applied STARRPeaker to comprehensively and unbiasedly call enhancers in them.
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http://dx.doi.org/10.1186/s13059-020-02194-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7722316PMC
December 2020

Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids.

Nat Commun 2020 10 19;11(1):5271. Epub 2020 Oct 19.

Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.

Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate preclinical research and personalized therapies. Our system provides combinatorial and dynamic drug treatments to hundreds of cultures and enables real-time analysis of organoids. We validate our system by performing individual, combinatorial, and sequential drug screens on human-derived pancreatic tumor organoids. We observe significant differences in the response of individual patient-based organoids to drug treatments and find that temporally-modified drug treatments can be more effective than constant-dose monotherapy or combination therapy in vitro. This integrated platform advances organoids models to screen and mirror real patient treatment courses with potential to facilitate treatment decisions for personalized therapy.
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http://dx.doi.org/10.1038/s41467-020-19058-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7573629PMC
October 2020

Corrugated Purple-Black Plaque on the Left Cheek: Challenge.

Am J Dermatopathol 2021 May;43(5):e54

Department of Dermatology, Oregon Health & Science University, Portland, OR.

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http://dx.doi.org/10.1097/DAD.0000000000001681DOI Listing
May 2021

Bariatric surgery decreases the number of first-time hospital admissions for cancer in severely obese patients. A retrospective analysis of the National Inpatient Sample database.

Surg Obes Relat Dis 2020 Nov 28;16(11):1648-1654. Epub 2020 Jul 28.

Department of General Surgery and the Bariatric and Metabolic Institute, Cleveland Clinic, Weston, Florida. Electronic address:

Background: According to the U.S. Centers for Disease Control, cancers linked to overweight or obesity accounted for roughly 40% of all U.S. malignancies in 2014.

Objectives: The primary aim of this epidemiologic study was to assess whether bariatric surgery might have any preventative role against obesity-linked cancers among individuals with obesity.

Setting: Hospitals across the United States participating in the National Inpatient Sample database, created, updated, and monitored by the U.S. Healthcare Cost and Utilization Project.

Methods: National Inpatient Sample data collected from 2010 to 2014 were examined to identify any difference in the number of first cancer-related hospitalizations, as a proxy for cancer incidence, between patients with a history of prior bariatric surgery (cases) and those without (controls). Patients with any prior cancer diagnosis were excluded. To match the body mass index ≥35 kg/m generally required for bariatric surgery, all controls had to have a body mass index ≥35 kg/m. International Classification of Diseases-9 codes were employed to identify admissions for 13 obesity-linked cancers. Multivariate logistic regression analysis was performed to identify any case-control differences, after matching for all baseline demographic, co-morbidity, and cancer risk-factor variables. All percentages and means (with confidence intervals) were weighted, per Healthcare Cost and Utilization Project guidelines.

Results: Among 1,590,579 controls and 247,015 bariatric surgery cases, there were 29,822 (1.93%; 95% confidence interval 1.91-1.96) and 3540 (1.43%; 1.38-1.47) first hospitalizations for cancer (adjusted odds ratio 1.17; 1.13-1.23; P < .0001).

Conclusions: Preliminary findings from a large U.S. database suggest that bariatric surgery may reduce the incidence of cancer in patients considered at high risk because of severe obesity.
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http://dx.doi.org/10.1016/j.soard.2020.07.017DOI Listing
November 2020

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Nature 2020 07 29;583(7818):699-710. Epub 2020 Jul 29.

Department of Biological Science, Florida State University, Tallahassee, FL, USA.

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE and Roadmap Epigenomics data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
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http://dx.doi.org/10.1038/s41586-020-2493-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410828PMC
July 2020

An integrative ENCODE resource for cancer genomics.

Nat Commun 2020 07 29;11(1):3696. Epub 2020 Jul 29.

Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.
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http://dx.doi.org/10.1038/s41467-020-14743-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391744PMC
July 2020

DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.

PLoS Comput Biol 2020 04 13;16(4):e1007522. Epub 2020 Apr 13.

Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.

Studies of complex disorders benefit from integrative analyses of multiple omics data. Yet, sample mix-ups frequently occur in multi-omics studies, weakening statistical power and risking false findings. Accurately aligning sample information, genotype, and corresponding omics data is critical for integrative analyses. We developed DRAMS (https://github.com/Yi-Jiang/DRAMS) to Detect and Re-Align Mixed-up Samples to address the sample mix-up problem. It uses a logistic regression model followed by a modified topological sorting algorithm to identify the potential true IDs based on data relationships of multi-omics. According to tests using simulated data, the more types of omics data used or the smaller the proportion of mix-ups, the better that DRAMS performs. Applying DRAMS to real data from the PsychENCODE BrainGVEX project, we detected and corrected 201 (12.5% of total data generated) mix-ups. Of the 21 mix-ups involving errors of racial identity, DRAMS re-assigned all data to the correct racial group in the 1000 Genomes project. In doing so, quantitative trait loci (QTL) (FDR<0.01) increased by an average of 1.62-fold. The use of DRAMS in multi-omics studies will strengthen statistical power of the study and improve quality of the results. Even though very limited studies have multi-omics data in place, we expect such data will increase quickly with the needs of DRAMS.
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http://dx.doi.org/10.1371/journal.pcbi.1007522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179940PMC
April 2020

Concordance between fMRI and Wada test for memory lateralization in temporal lobe epilepsy: A meta-analysis and systematic review.

Epilepsy Behav 2020 06 7;107:107065. Epub 2020 Apr 7.

Department of Clinical Neurological Sciences, Western University, London, Ontario, Canada; Department of Medical Biophysics, Western University, London, Ontario, Canada; Department of Medical Imaging, Western University, London, Ontario, Canada; Department of Psychology, Western University, London, Ontario, Canada.

Objective: The Wada test (WT) is increasingly being replaced by functional magnetic resonance imaging (fMRI) to evaluate memory lateralization before temporal lobe epilepsy (TLE) surgery. We aimed to determine, via meta-analysis, agreement between the two tests and identify predictors of disagreement.

Methods: We performed a systematic search for studies comparing WT and fMRI for memory lateralization with individual-patient data. If results were provided as laterality indexes instead of hemispheric lateralization, the cutoff point for memory lateralization was set to the usual ±2 for WT and ±0.20 for fMRI. We also evaluated results at our Epilepsy Center.

Results: Seven published series plus our own were included, comprising 124 patients. Wada test was performed by recognizing objects in half of the studies, and scenes, drawings, and words in the rest. All used scenes or pictures encoding for fMRI. Wada test-fMRI agreement across the studies ranged from 21.1 to 100%, averaging 46.8% (95% confidence interval [CI]: 37.6-56.0%). When cases with bilateral memory in either test were excluded, agreement reached 78.7% (95% CI: 67.6-89.8%), and concordance with contralateral TLE foci 86.4% for the WT and 83.0% for fMRI. Higher agreement was associated with using multiple items during WT (p = 0.001) and higher disagreement with presence of a lesion on MRI (p = 0.024). Binary logistic regression confirmed use of multiple items on WT as the strongest predictor of agreement (odds ratio [OR]: 6.95, 95% CI: 1.84-26.22; p = 0.004) and a bilateral result on the WT or fMRI of disagreement (OR: 0.24, 95% CI: 0.07-0.89 and OR: 0.12, 95% CI: 0.03-0.45; p < 0.05).

Conclusion: Concordance between WT and fMRI for memory lateralization is low in patients with TLE and bilateral memoryl memory distribution or a structural etiology, and it improves with encoding of a varied set of items. Both tests can help to lateralize the TLE foci.
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http://dx.doi.org/10.1016/j.yebeh.2020.107065DOI Listing
June 2020

Ulcerative C2 neurocutaneous dysesthesia (trigeminal trophic syndrome in an alternative distribution).

Dermatol Online J 2020 Jan 15;26(1). Epub 2020 Jan 15.

Department of Dermatology, Oregon Health & Science University, Portland, OR.

Trigeminal trophic syndrome is an uncommon condition characterized by paresthesia, itch, and self-inflicted wounds following the trigeminal dermatome(s). Similar processes adhering to cervical nerve distributions have been reported, calling into question the specificity of trigeminal trophic syndrome for the trigeminal network. Herein, we report patient with trigeminal trophic syndrome adhering to the C2 dermatome, a previously unreported distribution.
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January 2020

IFSO (International Federation for Surgery of Obesity and Metabolic Disorders) Consensus Conference Statement on One-Anastomosis Gastric Bypass (OAGB-MGB): Results of a Modified Delphi Study.

Obes Surg 2020 May;30(5):1625-1634

Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

Background: One-anastomosis gastric bypass (OAGB-MGB) is currently the third performed primary bariatric surgical procedure worldwide. However, the procedure is hampered by numerous controversies and there is considerable variability in surgical technique, patient selection, and pre- and postoperative care among the surgeons performing this procedure. This paper reports the results of a modified Delphi consensus study organized by the International Federation for Surgery of Obesity and Metabolic Disorders (IFSO).

Methods: Fifty-two internationally recognized bariatric experts from 28 countries convened for voting on 90 consensus statements over two rounds to identify those on which consensus could be reached. Inter-voter agreement of ≥ 70% was considered consensus, with voting participation ≥ 80% considered a robust vote.

Results: At least 70% consensus was achieved for 65 of the 90 questions (72.2% of the items), 61 during the first round of voting and an additional four in the second round. Where consensus was reached on a binary agree/disagree or yes/no item, there was agreement with the statement presented in 53 of 56 instances (94.6%). Where consensus was reached on a statement where options favorable versus unfavorable to OAGB-MGB were provided, including statements in which OAGB-MGB was compared to another procedure, the response option favorable to OAGB-MGB was selected in 13 of 23 instances (56.5%).

Conclusion: Although there is general agreement that the OAGB-MGB is an effective and usually safe option for the management of patients with obesity or severe obesity, numerous areas of non-consensus remain in its use. Further empirical data are needed.
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http://dx.doi.org/10.1007/s11695-020-04519-yDOI Listing
May 2020

The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development.

Nucleic Acids Res 2020 04;48(7):3476-3495

Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.

The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers depending on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.
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http://dx.doi.org/10.1093/nar/gkaa082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144903PMC
April 2020

Shared Molecular Neuropathology Across Major Psychiatric Disorders Parallels Polygenic Overlap.

Focus (Am Psychiatr Publ) 2019 Jan 7;17(1):66-72. Epub 2019 Jan 7.

(Gandal et al., "Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap" Science 09 Feb 2018:Vol. 359, Issue 6376, pp. 693-697 (DOI: 10.1126/science.aad6469). Reprinted with permission from AAAS).
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http://dx.doi.org/10.1176/appi.focus.17103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6996074PMC
January 2019

Retrospective Cohort: Genomic Differences Between Pigmented Spindle Cell Nevi of Reed and Reed-Like Melanomas.

Am J Dermatopathol 2020 Sep;42(9):641-647

Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL.

Background: Some melanomas closely resemble pigmented spindle cell nevi (PSCN) of Reed histologically. The distinction of these entities is important for clinical management. A recent study showed most PSCN (78%) are fusion-driven, commonly involving NTRK3 (57%). Conversely, BRAF V600E mutations are not characteristic of PSCN but are frequent in melanoma.

Objective: In this study, we assessed clinical, histologic and genomic differences between PSCN of Reed and Reed-like melanomas (RLMs).

Methods: We performed BRAF V600E immunohistochemistry (IHC) for 18 PSCN and 20 RLM cases. All 23 benign PSCN cases previously underwent whole transcriptome and targeted DNA sequencing with a 1711 gene panel.

Results: We previously demonstrated the majority of PSCN (18 of 23) has chimeric fusions. Among PSCN without a chimeric fusion, BRAF mutations were common. Noncanonical BRAF mutations were identified in 2 of 5 nonfusion cases, and 1 case had a canonical BRAF mutation. Alternatively, 70% of RLM demonstrated a BRAF V600E mutation. RLM also occurred more frequently in older patients.

Limitations: The overall sample size was small.

Conclusions: In diagnostically challenging cases, ancillary IHC studies can assist in distinguishing PSCN from RLM. Our study suggests positive staining by IHC for BRAF V600E and older age strongly favors a diagnosis of RLM.
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http://dx.doi.org/10.1097/DAD.0000000000001603DOI Listing
September 2020
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