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Item Consensus molecular subtyping of colorectal cancers is influenced by goblet cell content(Elsevier, 2021) Miller, Samuel A.; Ghobashi, Ahmed H.; O'Hagan, Heather M.; Medical and Molecular Genetics, School of MedicineA critical obstacle in the field of colorectal cancer (CRC) is the establishment of precise tumor subtypes to facilitate the development of targeted therapeutic regimens. While dysregulated mucin production is a histopathological feature of multiple CRC subtypes, it is not clear how well these pathologies are associated with the proportion of goblet cells in the tumor, or whether or not this proportion is variable across all CRC. This study demonstrates that consensus molecular subtype 3 (CMS3) CRC tumors and cell lines are enriched for the expression of goblet cell marker genes. Further, the proportion of goblet cells in the tumor is associated with the probability of CMS3 subtype assignment and these CMS3 subtype tumors are mutually exclusive from mucinous adenocarcinoma pathologies. This study provides proof of principle for the use of machine learning classification systems to subtype tumors based on cellular content, and provides further context regarding the features weighing CMS3 subtype assignment.Item A brother and sister with the same karyotype: Case report of two siblings with partial 3p duplication and partial 9p deletion and sex reversal(Wiley, 2021-05-06) Selby, Susan Cordes; Iwata-Otsubo, Aiko; Delk, Paula; Nebesio, Todd D.; Gohil, Anisha; Matlock, Peggy; Torres-Martinez, Wilfredo; Vance, Gail H.; Medical and Molecular Genetics, School of MedicineTwo siblings with the same male unbalanced karyotype demonstrate sex reversal. The older sib appeared phenotypically female and the younger sib demonstrated a male gender. The female had gonadal dysgenesis with bilateral ovatestes. The male had bilateral testes. The report discusses the phenotypical differences and genes associated with sex reversal.Item Genetic Variation and Immunohistochemical Localization of the Glucocorticoid Receptor in Breast Cancer Cases from the Breast Cancer Care in Chicago Cohort(MDPI, 2021-05) Al-Alem, Umaima; Mahmoud, Abeer M.; Batai, Ken; Shah-Williams, Ebony; Gann, Peter H.; Kittles, Rick; Rauscher, Garth H.; Medical and Molecular Genetics, School of MedicineBackground: Glucocorticoid, one of the primary mediators of stress, acts via its receptor, the glucocorticoid receptor (GCR/NR3C1), to regulate a myriad of physiological processes. We measured the genetic variation and protein expression of GCR, and the genes that regulate GCR function or response and examined whether these alterations were associated with breast cancer clinicopathological characteristics. Method: We used samples from a multiracial cohort of breast cancer patients to assess the association between breast cancer characteristics and the genetic variants of single nucleotide polymorphisms (SNPs) in GCR/NR3C1, FKBP5, Sgk1, IL-6, ADIPOQ, LEPR, SOD2, CAT, and BCL2. Results: Several SNPs were associated with breast cancer characteristics, but statistical significance was lost after adjustment for multiple comparisons. GCR was detected in all normal breast tissues and was predominantly located in the nuclei of the myoepithelial cell layer, whereas the luminal layer was negative for GCR. GCR expression was significantly decreased in all breast cancer tissue types, compared to nontumor tissue, but was not associated with breast cancer characteristics. We found that high nuclear GCR expression was associated with basal cell marker cytokeratin 5/6 positivity. Conclusion: GCR expression is reduced in breast cancer tissue and correlates with the basal cell marker CK5/6.Item Report of New Haplotype for ABCC2 Gene rs17222723 and rs8187718 in cis(Elsevier, 2015-03-01) Pratt, Victoria M.; Beyer, Brittany N.; Koller, Daniel L.; Skaar, Todd C.; Flockhart, David A.; Levy, Kenneth D.; Vance, Gail H.; Medical and Molecular Genetics, School of MedicineThe ATP-binding cassette, subfamily C [CFTR/MRP], member 2 (ABCC2) gene is a member of the ATP-binding cassette transporters and is involved in the transport of molecules across cellular membranes. Substrates transported by ABCC2 include antiepileptics, statins, tenofovir, cisplatin, irinotecan, and carbamazepine. Because of the pharmacogenomics implications, we developed a clinical laboratoryedeveloped assay to test for seven variants in the ABCC2 gene: c.3563T>A (p.V1188E, rs17222723), c.1249G>A (p.V417I, rs2273697), c.3972C>T (p.I1324I, rs3740066), c.2302C>T (p.R768W, rs56199535), c.2366C>T (p.S789F, rs56220353), c.-24C>T (50 UTR, rs717620), and c.4544G>A (p.C1515Y, rs8187710). During the validation process, we noted several DNA samples, obtained from the Coriell Cell Repository, that contained both c.3563T>A, c.4544G>A, and a third variant, suggesting that c.3563T>A and c.4544G>A are in cis on the chromosome in some individuals. We obtained DNA samples from a trio (father, mother, and child), tested their ABCC2 variants, and confirmed that c.3563T>A and c.4544G>A were in cis on the same chromosome. Here, we report a new haplotype in ABCC2. (J Mol Diagn 2015, 17: 201e205; http://dx.doi.org/10.1016/ j.jmoldx.2014.11.005)Item Cross-Sectional Exploration of Plasma Biomarkers of Alzheimer's Disease in Down Syndrome: Early Data from the Longitudinal Investigation for Enhancing Down Syndrome Research (LIFE-DSR) Study(MDPI, 2021-04-28) Hendrix, James A.; Airey, David C.; Britton, Angela; Burke, Anna D.; Capone, George T.; Chavez, Ronelyn; Chen, Jacqueline; Chicoine, Brian; Costa, Alberto C.S.; Dage, Jeffrey L.; Doran, Eric; Esbensen, Anna; Evans, Casey L.; Faber, Kelley M.; Foroud, Tatiana M.; Hart, Sarah; Haugen, Kelsey; Head, Elizabeth; Hendrix, Suzanne; Hillerstrom, Hampus; Kishnani, Priya S.; Krell, Kavita; Ledesma, Duvia Lara; Lai, Florence; Lott, Ira; Ochoa-Lubinoff, Cesar; Mason, Jennifer; Nicodemus-Johnson, Jessie; Proctor, Nicholas Kyle; Pulsifer, Margaret B.; Revta, Carolyn; Rosas, H. Diana; Rosser, Tracie C.; Santoro, Stephanie; Schafer, Kim; Scheidemantel, Thomas; Schmitt, Frederick; Skotko, Brian G.; Stasko, Melissa R.; Talboy, Amy; Torres, Amy; Wilmes, Kristi; Woodward, Jason; Zimmer, Jennifer A.; Feldman, Howard H.; Mobley, William; Medical and Molecular Genetics, School of MedicineWith improved healthcare, the Down syndrome (DS) population is both growing and aging rapidly. However, with longevity comes a very high risk of Alzheimer's disease (AD). The LIFE-DSR study (NCT04149197) is a longitudinal natural history study recruiting 270 adults with DS over the age of 25. The study is designed to characterize trajectories of change in DS-associated AD (DS-AD). The current study reports its cross-sectional analysis of the first 90 subjects enrolled. Plasma biomarkers phosphorylated tau protein (p-tau), neurofilament light chain (NfL), amyloid β peptides (Aβ1-40, Aβ1-42), and glial fibrillary acidic protein (GFAP) were undertaken with previously published methods. The clinical data from the baseline visit include demographics as well as the cognitive measures under the Severe Impairment Battery (SIB) and Down Syndrome Mental Status Examination (DS-MSE). Biomarker distributions are described with strong statistical associations observed with participant age. The biomarker data contributes to understanding DS-AD across the spectrum of disease. Collectively, the biomarker data show evidence of DS-AD progression beginning at approximately 40 years of age. Exploring these data across the full LIFE-DSR longitudinal study population will be an important resource in understanding the onset, progression, and clinical profiles of DS-AD pathophysiology.Item Single cell transcriptome profiling of the human alcohol-dependent brain(Oxford University Press, 2020-05-08) Brenner, Eric; Tiwari, Gayatri R.; Kapoor, Manav; Liu, Yunlong; Brock, Amy; Mayfield, R. Dayne; Medical and Molecular Genetics, School of MedicineAlcoholism remains a prevalent health concern throughout the world. Previous studies have identified transcriptomic patterns in the brain associated with alcohol dependence in both humans and animal models. But none of these studies have systematically investigated expression within the unique cell types present in the brain. We utilized single nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of over 16 000 nuclei isolated from the prefrontal cortex of alcoholic and control individuals. Each nucleus was assigned to one of seven major cell types by unsupervised clustering. Cell type enrichment patterns varied greatly among neuroinflammatory-related genes, which are known to play roles in alcohol dependence and neurodegeneration. Differential expression analysis identified cell type-specific genes with altered expression in alcoholics. The largest number of differentially expressed genes (DEGs), including both protein-coding and non-coding, were detected in astrocytes, oligodendrocytes and microglia. To our knowledge, this is the first single cell transcriptome analysis of alcohol-associated gene expression in any species and the first such analysis in humans for any addictive substance. These findings greatly advance the understanding of transcriptomic changes in the brain of alcohol-dependent individuals.Item Umbilical cord blood transplantation in adults: Results of the prospective cord blood transplantation (COBLT)(ScienceDirect, 2005-02-01) Cornetta, Kenneth; Laughlin, Mary; Carter, Shelly; Wall, Donna; Weinthal, Joel; Delaney, Colleen; Wagner, John; Sweetman, Robert; McCarthy, Philip; Chao, Nelson; Medical and Molecular Genetics, School of MedicineThe Cord Blood Transplantation study group conducted a prospective study of unrelated cord blood transplantation (CBT) to better define the role of this stem cell source for subjects requiring unrelated allogeneic transplantation. We report on 1 stratum of the study designated for adult subjects. The primary end point of the study was survival at 180 days. Secondary end points included engraftment, graft-versus-host disease, relapse, and long-term survival. Eligibility criteria for malignant and nonmalignant diseases were specified. Subjects with active central nervous system disease, Karnofsky performance status <70%, grade 3 or 4 or primary myelofibrosis, or suitable related donors were excluded. Enrollment required a single cord blood unit containing >107 nucleated cells per kilogram of recipient weight and matched at ≥4 HLA-A and -B (low or intermediate resolution) and -DRB1 (high resolution) types. Thirty-four subjects were entered, with a median age of 34.5 years (range, 18.2-55 years). Most subjects (n = 23) had a 4 of 6 match, 10 subjects had a 5 of 6 match, and 1 subject had a 6 of 6 match. Diagnoses at transplantation included acute myelogenous leukemia (n = 19), acute lymphoblastic leukemia (n = 9), chronic myelogenous leukemia (n = 3), myelodysplastic syndrome (n = 1), paroxysmal nocturnal hemoglobinuria (PNH) (n = 1), and non-Hodgkin lymphoma (n = 1); 94% were classified as poor risk according to National Marrow Donor Program criteria. Subjects received total body irradiation/cyclophosphamide (n = 27) or busulfan/melphalan (n = 7) conditioning regimens. Four subjects died before CBT and are described here but are not included in the main analysis. The cumulative incidence rates and median times to neutrophil (500/μL) and platelet (>20 000/μL) engraftment were 0.66 by day 42 (median, 31 days) and 0.35 by day 180 (median, 117 days). The cumulative incidence rate for grade II-IV GVHD was 0.34 by day 100. For the primary end point, survival at 180 days, Kaplan-Meier survival estimates were 0.30 (95% confidence interval, 0.14-0.46) by day 180 after transplantation. To date there are 2 survivors, and both are >36 months from enrollment. A retrospective analysis was performed by using high-resolution HLA-A and -B typing, which revealed that approximately one third of subjects had 1 or more additional HLA mismatches compared with results of low- or intermediate-resolution HLA typing. The findings of high treatment-related mortality and slow engraftment kinetics indicate that CBT should continue to be performed in specialized centers with a research focus on cord blood cells.Item Genetic counseling for advanced paternal age: A survey of genetic counselors' current practice(Wiley, 2021-04) Quirin, Kayla; Hines, Karrie A.; Wetherill, Leah; Medical and Molecular Genetics, School of MedicineAdvanced paternal age (APA) has no formal definition, though many publications utilize the cutoff of fathers >40 years of age. The literature demonstrates an association between APA and certain conditions including de novo autosomal dominant disorders, birth defects, and neuropsychiatric conditions. This study surveyed 165 genetic counselors within the National Society of Genetic Counselors to assess their current approach to APA. t Tests, analysis of variance, logistic regression, and chi-squared tests were performed on quantitative data, and content analysis was applied to qualitative data. Although most respondents have discussed APA with a patient (88%), there was no consensus on what age cutoff constitutes APA: >40 (N = 53, 37.9%), >45 (N = 61, 43.6%), >50 (N = 24, 17.1%), or >55 (N = 2, 1.4%). Those who discussed APA were more likely to be prenatal counselors, see more patients per week, be board certified, or be familiar with current APA guidelines. Respondents agreed the literature supports the association of APA with deleterious outcomes (mean agreement = 8.2, median = 8 on a 1 = strongly disagree to 10 = strongly agree). Individuals who discussed APA and were board certified had higher agreement. Content analysis confirmed agreement that the literature supports an association between APA and deleterious outcomes (documented in responses from 31.5% of prenatal respondents, 17.8% others) but noted that available testing and screening options for associated conditions are limited (34.4% of prenatal respondents, 17.4% others). Prenatal and non-prenatal respondents reported similar agreement with the statement that APA is associated with deleterious outcomes. However, most non-prenatal respondents were unfamiliar with current guidelines (80%), and presumably as a result, were also less likely to discuss APA with their patients. Our study identified a need to disseminate information regarding APA and current guidelines to genetic counselors, particularly non-prenatal and those with less experience.Item Transcriptome Landscape of Epithelial to Mesenchymal Transition of Human Stem Cell–Derived RPE(Association for Research in Vision and Ophthalmology, 2021-04) Sripathi, Srinivasa R.; Hu, Ming-Wen; Liu, Melissa M.; Wan, Jun; Cheng, Jie; Duan, Yukan; Mertz, Joseph L.; Wahlin, Karl J.; Maruotti, Julien; Berlinicke, Cynthia A.; Qian, Jiang; Zack, Donald J.; Medical and Molecular Genetics, School of MedicinePurpose: RPE injury often induces epithelial to mesenchymal transition (EMT). Although RPE-EMT has been implicated in a variety of retinal diseases, including proliferative vitroretinopathy, neovascular and atrophic AMD, and diabetic retinopathy, it is not well-understood at the molecular level. To contribute to our understanding of EMT in human RPE, we performed a time-course transcriptomic analysis of human stem cell-derived RPE (hRPE) monolayers induced to undergo EMT using 2 independent, yet complementary, model systems. Methods: EMT of human stem cell-derived RPE monolayers was induced by either enzymatic dissociation or modulation of TGF-β signaling. Transcriptomic analysis of cells at different stages of EMT was performed by RNA-sequencing, and select findings were confirmed by reverse transcription quantitative PCR and immunostaining. An ingenuity pathway analysis (IPA) was performed to identify signaling pathways and regulatory networks associated with EMT. Results: Proteocollagenolytic enzymatic dissociation and cotreatment with TGF-β and TNF-α both induce EMT in human stem cell-derived RPE monolayers, leading to an increased expression of mesenchymal factors and a decreased expression of RPE differentiation-associated factors. Ingenuity pathway analysis identified the upstream regulators of the RPE-EMT regulatory networks and identified master switches and nodes during RPE-EMT. Of particular interest was the identification of widespread dysregulation of axon guidance molecules during RPE-EMT progression. Conclusions: The temporal transcriptome profiles described here provide a comprehensive resource of the dynamic signaling events and the associated biological pathways that underlie RPE-EMT onset. The pathways defined by these studies may help to identify targets for the development of novel therapeutic targets for the treatment of retinal disease.Item Use of amplicon-based sequencing for testing fetal identity and monogenic traits with Single Circulating Trophoblast (SCT) as one form of cell-based NIPT(PLOS, 2021-04-15) Zhuo, Xinming; Wang, Qun; Vossaert, Liesbeth; Salman, Roseen; Kim, Adriel; Van den Veyver, Ignatia; Breman, Amy; Beaudet, Arthur; Medical and Molecular Genetics, School of MedicineA major challenge for cell-based non-invasive prenatal testing (NIPT) is to distinguish individual presumptive fetal cells from maternal cells in female pregnancies. We have sought a rapid, robust, versatile, and low-cost next-generation sequencing method to facilitate this process. Toward this goal, single isolated cells underwent whole genome amplification prior to genotyping. Multiple highly polymorphic genomic regions (including HLA-A and HLA-B) with 10-20 very informative single nucleotide polymorphisms (SNPs) within a 200 bp interval were amplified with a modified method based on other publications. To enhance the power of cell identification, approximately 40 Human Identification SNP (Applied Biosystems) test amplicons were also utilized. Using SNP results to compare to sex chromosome data from NGS as a reliable standard, the true positive rate for genotyping was 83.4%, true negative 6.6%, false positive 3.3%, and false negative 6.6%. These results would not be sufficient for clinical diagnosis, but they demonstrate the general validity of the approach and suggest that deeper genotyping of single cells could be completely reliable. A paternal DNA sample is not required using this method. The assay also successfully detected pathogenic variants causing Tay Sachs disease, cystic fibrosis, and hemoglobinopathies in single lymphoblastoid cells, and disease-causing variants in three cell-based NIPT cases. This method could be applicable for any monogenic diagnosis.