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Abstract PD15-12: PD15-12 A pre-surgical window trial of oral tamoxifen versus transdermal 4-hydroxytamoxifen gel in women with estrogen receptor positive duct carcinoma in situ (DCIS)
Lee, Oukseub , Mi, Xinlei , Xu, Yanfei , Blanco, Luis Z. , Akasha, Azza M., Zhang, Shanshan , LaBoy, Carissa , Helland, Thomas , Al‐Hilli, Zahraa , Hwang, E. Shelley, Guenther, Joseph M., Hustad, Simon Steinar, Gursel, Demirkan, Kocherginsky, Masha , Perloff, Marjorie , Benante, Kelly A. , Pilewskie, Melissa , Degnim, Amy C. , Amin, Amanda Leigh , Mellgren, Gunnar , Dimond, Eileen P. , Perloff, Marjorie, Heckman‐Stoddard, Brandy M. , Khan, Seema A.

Cancer Research | March 2, 2023 | Volume: 83 | Issue: 5_Supplement | Pages: PD15-12-PD15-12

10.1158/1538-7445.sabcs22-pd15-12 Get It

Abstract Background: Adjuvant oral tamoxifen (TAM) benefits women with DCIS, but toxicity concerns have limited its acceptance. Transdermal therapy with 4-hydroxy tamoxifen (4-OHT) gel applied to the breast skin is a possible solution. Previous pilot data suggest equivalent anti-proliferative efficacy of TAM and 4-OHT gel, but minimal systemic exposure with transdermal therapy. We report a prospective double blinded randomized phase 2 trial comparing TAM to 4-OHT gel in women with DCIS. Methods: 107 women with estrogen receptor positive (≥10%) DCIS were randomized to TAM (20 mg/day + placebo gel) or 4-OHT gel (2mg 4-OHT gel/breast, bilaterally + oral placebo), for 4-10 weeks prior to surgery. The primary endpoint was reduction in DCIS Ki67 labeling index (LI). Secondary endpoints included the 12-gene DCIS Score assay (Exact Sciences), breast tissue and plasma concentrations of 4-OHT and endoxifen, TAM-responsive circulating proteins, and patient reported symptoms (Breast Eight Symptom Scale). We estimated that 80 evaluable participants would provide 80.5% power to establish non-inferiority of 4-OHT, defined as relative Ki67-LI decline >35% and absolute decline >2.6%, with one-sided 𝛼=0.10. Non-inferiority of 4-OHT gel for Ki67-LI reduction was tested using an ANCOVA model. Statistical comparisons within- and between-arms were calculated with paired t-test and Welch Two Sample t-test, respectively. Results: 72 of 87 women adhered to the protocol, and were evaluable for the primary endpoint (39 TAM and 33 4-OHT gel). Mean treatment duration was 47 days for TAM and 44 days for 4-OHT gel (p=0.2). The median absolute decline in Ki67 labeling index was significant in the oral TAM (-3.7%, p< 0.001) but not in 4-OHT gel arm (-1.3%, p=0.2) (p=0.002). Ki67 results following menopausal stratification also favored the TAM arm: (-1.3%; p=0.06 in 37 premenopausal women and -3.7%; p=0.02 in 35 postmenopausal women). Similarly, DCIS score showed a significantly greater reduction in the TAM (-14, p< 0.001) but not in the 4-OHT gel arm (-4, p=0.1). Tissue 4-OHT concentrations were non-significantly higher in the TAM arm and were similar between superficial and deep sampling locations (superficial 6.1 and 4.2 ng/g for TAM and 4-OHT gel, respectively, p= 0.55; deep 5.7 and 3.8 ng/g, respectively, p= 0.06), whereas plasma 4-OHT concentration was markedly lower in the gel group (2 ng/mL and 0.24 ng/mL for TAM and 4-OHT gel, respectively, P < 0.001). Endoxifen was abundant in plasma (11 ng/mL) and deep tissue (13 ng/g) of the TAM arm, but present in trace amounts in the 4-OHT gel arm (undetectable in plasma and 0.31 ng/g in tissue; p < 0.001). Circulating TAM responsive markers (insulin like growth factor 1, sex hormone binding globulin, von Willebrand factor, and protein S total) and vasomotor symptoms were significantly and unfavorably modulated by TAM, but not by 4-OHT gel therapy. Conclusions: The non-inferiority of transdermal 4-OHT gel to Tam in terms of anti-proliferative effect in DCIS lesions was not demonstrated at the doses used for this study. DCIS Score analysis gave similar results. Tissue 4-OHT concentration in 4-OHT gel and Tam-treated subjects was roughly similar. However, endoxifen exposure was higher with oral TAM therapy and may partially explain the observed differences in major endpoints. In future studies, use of higher 4-OHT gel doses, longer duration of treatment, or different formulation may overcome these. Citation Format: Oukseub Lee, Xinlei Mi, Yanfei Xu, Luis Blanco, Azza M. Akasha, Kelly Benante, Shanshan Zhang, Carissa LaBoy, Thomas Helland, Melissa Pilewskie, Amy Degnim, Zahraa Al-Hilli, Amanda L. Amin, E Shelley Hwang, Joseph M. Guenther, Simon Steinar Hustad, Demirkan B. Gursel, Masha Kocherginsky, Gunnar Mellgren, Eileen Dimond, Marjorie Perloff, Brandy M. Heckman-Stoddard, Seema Khan. PD15-12 A pre-surgical window trial of oral tamoxifen versus transdermal 4-hydroxytamoxifen gel in women with estrogen receptor positive duct carcinoma in situ (DCIS) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD15-12.
Abstract P1-07-02: Using clinical characteristics and molecular markers to predict the risk of subsequent ipsilateral breast events after excision of DCIS
King, Lorraine , Harmon, Bryan, Gallagher, Kristalyn K. , Kilgore, Mark , Wei, Shi, King, Tari A. , McAuliffe, Priscilla F. , Hwang, Esther , Liu, Ying , Strand, Siri H. , Couch, Fergus J. , DeMichele, Angela , Marks, Jeffrey R. , Maley, Carlo C. , West, Robert B. , Colditz, Graham A.

Cancer Research | March 2, 2023 | Volume: 83 | Issue: 5_Supplement | Pages: P1-07-02-P1-07-02

10.1158/1538-7445.sabcs22-p1-07-02 Get It

Abstract PURPOSE To examine incremental values of estrogen receptor (ER) status, body mass index (BMI), menopausal status, and a previously reported multi-gene classifier over commonly used clinical factors (i.e. age, tumor grade, comedonecrosis, surgical margins, and treatment) in predicting risk of any ipsilateral recurrence (IR) event within five years after DCIS diagnosis. METHODS A derivation cohort consisted of participants in the Translational Breast Cancer Research Consortium (TBCRC) 038, a retrospective multicenter cohort study in women undergoing surgical resection for DCIS between 01/01/1998 and 02/29/2016 (n=216). The validation cohort, the Repository of Archival Human Breast Tissue (RAHBT) at Washington University School of Medicine, provided cases meeting the same eligibility criteria as TBCRC038 (n=97). Participants in both cohorts had RNA-seq data and either developed IR 1-5y after initial DCIS diagnosis or were free from subsequent breast events for at least five years. The previously reported 812-gene classifier had been developed from a subset of the TBCRC038 samples using a negative-binomial regression model to identify differentially expressed genes in the primary tumor associated with subsequent recurrence events. This classifier has been shown to be highly correlated with 5-year invasive, DCIS, and all breast cancer events, and validated in the RAHBT cohort. Cox proportional hazards regression was used to estimate hazard ratios (HRs) of IR in the TBCRC038 cohort (76 with IR). The clinical score was developed using clinical predictors (aforementioned clinical factors and ER) and their regression coefficients from the model with the maximum predictive accuracy (e.g. c-index) and the minimum number of predictors; the summary score integrated the clinical score and multi-gene classifier. Predictive performance of both clinical and summary scores was validated in the RAHBT cohort (20 with IR). RESULTS In the TBCRC cohort derivation set, we used a multivariable model based on clinical factors alone (clinical score) and found that ER status, but not BMI or menopausal status, was independently associated with a higher IR risk (HR=2.06, 95% CI 1.18-3.58). Adding the multi-gene classifier to the clinical factors-based model (summary score) in the TBCRC038 test set increased predictive accuracy (c-index 0.68 to 0.70), with the genomic classifier-adjusted HR of 14.96 (95% CI 8.64-25.91). The summary score had higher predictive performance for IR risk than clinical score alone (c-index 0.82 vs. 0.70). In the RAHBT validation samples, model performance was similarly improved using summary scores clinical factors-based model plus multigene classifier as compared to clinical scores along (c-index 0.74 vs. 0.58). CONCLUSION Combining clinical factors and a multigene classifier provided more accurate risk estimates of IR within five years after excision of DCIS than clinical factors alone. Figure 1. Observed and predicted recurrence-free survival in the first five years after initial DCIS diagnosis in the RAHBT validation cohort, by risk groups defined by clinical scores (left) and clinical score plus multigene classifier (right). Citation Format: Ying Liu, Siri H. Strand, Lorraine King, Bryan Harmon, Fergus J. Couch, Kristalyn Gallagher, Mark Kilgore, Shi Wei, Angela DeMichele, Tari King, Priscilla F. McAuliffe, Jeffrey Marks, Carlo Maley, Robert West, E Shelley Hwang, Graham A. Colditz. Using clinical characteristics and molecular markers to predict the risk of subsequent ipsilateral breast events after excision of DCIS [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-07-02.
Abstract GS4-02: Oncological Outcomes Following Omission of Axillary Lymph Node Dissection in Node Positive Patients Downstaging To Node Negative with Neoadjuvant Chemotherapy: the OPBC-04/EUBREAST-06/OMA study
Montagna, Giacomo , Mrdutt, Mary M., Botty, Astrid, Hwang, E. Shelley, Ingham, Abigail, Papassotiropoulos, Bärbel , Kurzeder, Christian , Aybar, Danilo Díaz, Vorburger, Denise , Matlac, Dieter Michael, Fitzal, Florian , Meani, Francesco , Fick, Franziska, Sagasser, Jacqueline, Heil, Jörg, Dedes, Konstantin J. , Romics, László , Banys‐Paluchowski, Maggie , Pérez, María del Rosario Cueva, Fehr, Mathias K. , Ditsch, Nina , Zarhi, Sebastián Solé, Küemmel, Sherko, Bruz̆as, S., Parissenti, Tamara K., Güth, Uwe , Ovalle, Valentina , Tausch, Christoph, Morrow, Monica , Kühn, Thorsten, Barrio, Andrea V. , Sevilimedu, Varadan , Boughey, Judy C. , Hoskin, Tanya L. , Rosenberger, Laura H. , Nguyen-Sträuli, Bich Doan , Matlac, Dieter Michael , Ostapenko, Edvin , Riedel, Fabian , Heil, Joerg , Díaz, Marcelo Chávez , Heidinger, Martin , Reinisch, Mattea , Maggi, Nadia , Rocco, Nicola , Gentilini, Oreste D , Paulinelli, Régis Resende , Lascio, Simona Di , Weber, William P.

Cancer Research | March 2, 2023 | Volume: 83 | Issue: 5_Supplement | Pages: GS4-02-GS4-02

10.1158/1538-7445.sabcs22-gs4-02 Get It

Abstract Background: Data on the oncologic safety of omission of axillary lymph node dissection (ALND) in node positive (N+) patients who downstage to ypN0 with neoadjuvant chemotherapy (NAC) is sparse. Additionally, there is no consensus on which axillary staging procedure should be used in this setting, sentinel lymph node biopsy (SLNB) alone or in combination with localization and retrieval of the clipped positive node, also known as targeted axillary dissection (TAD). Whether the reduction in the false negative rate observed with TAD translates into a significant reduction in the rate of axillary recurrence is unknown. We sought to evaluate oncologic outcomes after omission of ALND in a large, real-world cohort of breast cancer (BC) patients and to compare rates of axillary recurrence after SLNB with dual tracer mapping vs. TAD. Methods: Data were collected from 19 centers in the Oncoplastic Breast Consortium (OPBC) and EUBREAST networks. Patients with T1-4 biopsy-proven N1-3 BC who underwent NAC followed by axillary staging with either SLNB with dual tracer mapping or TAD and who were pathologically node negative (ypN0) were included. ypN0 was defined as the absence of any tumor or isolated tumor cells. Competing risk analysis was performed to assess the cumulative incidence rates of axillary recurrence, locoregional recurrence, and any invasive (locoregional or distant) recurrence. Two-year cumulative incidence rates were compared between TAD and SLNB using the Gray’s test. Type I error rate was set to 0.05 (α). Results: We included 785 patients (565 treated with SLNB and 220 with TAD) treated with NAC followed by surgery from 01/2014-12/2020. Median patient age was 50 years. The majority (57%) of patients had clinical T2 tumors, and 95% had N1 disease. Most (55%) were HER2+, and 21% were triple negative. Most patients (81%) received anthracycline and taxane-based chemotherapy regimens, but NAC regimens differed between patients treated with TAD and those treated with SLNB (Table 1). All patients with HER2+ tumors received anti HER2 therapy. Nodal radiotherapy was administered to 76% of patients, and was more common in patients who underwent TAD (82% TAD vs 74% SLNB, p=0.017). Breast pathologic complete response (ypT0/is) was more frequent among those patients that had TAD (80% TAD vs. 66% SLNB, p< 0.001). TAD localization was with wire in 46%, radioactive seed in 40%, ultrasound in 5%, tattoo in 2%, and with a combination of these techniques in 7%. The clipped node was successfully retrieved in 94% of TAD cases. The median number of lymph nodes removed was lower in the TAD group compared to the SLNB group [3 (IQR 3-5) vs 4 IQR 3-5), p< 0.001], as was the median number of sentinel lymph nodes [3 (IQR 2-4) vs 4 IQR 3-5), p< 0.001] (Table 1). The 5-year rates of any axillary recurrence, locoregional recurrence, and any invasive recurrence in the entire cohort were 1.1% (95%CI 0.39-2.4%), 3.1% (95%CI 1.6-5.3%) and 10% (95%CI 7.6-13%), respectively. The two-year cumulative incidence of axillary recurrence did not differ between patients treated with TAD compared to SLNB (0% vs 0.9%, p=0.19). Conclusion: Early axillary recurrence after omission of ALND in patients who successfully downstage from N+ to ypN0 with NAC is a rare event following both SLNB or TAD, and was not significantly lower in TAD than SLNB. Although longer follow-up is needed to confirm these findings, the main advantage of TAD seems to be a reduction in the number of lymph nodes removed. Overall, these results support omission of ALND in patients who successfully downstage to node negative disease after NAC. Table 1: Clinicopathological Features of the Study Cohort, Stratified by Axillary Staging Technique Citation Format: Giacomo Montagna, Mary Mrdutt, Astrid Botty, Andrea V. Barrio, Varadan Sevilimedu, Judy C. Boughey, Tanya L. Hoskin, Laura H. Rosenberger, E Shelley Hwang, Abigail Ingham, Bärbel Papassotiropoulos, Bich Doan Nguyen-Sträuli, Christian Kurzeder, Danilo Diaz Aybar, Denise Vorburger, Dieter Michael Matlac, Edvin Ostapenko, Fabian Riedel, Florian Fitzal, Francesco Meani, Franziska Fick, Jacqueline Sagasser, Jörg Heil, Konstantin J. Dedes, Laszlo Romics, Maggie Banys-Paluchowski, Maria Del Rosario Cueva Perez, Marcelo Chavez Diaz, Martin Heidinger, Mathias K. Fehr, Mattea Reinisch, Nadia Maggi, Nicola Rocco, Nina Ditsch, Oreste Davide Gentilini, Regis Resende Paulinelli, Sebastian Sole Zarhi, Sherko Küemmel, Simona Bruzas, Simona Di Lascio, Tamara Parissenti, Uwe Güth, Valentina Ovalle, Christoph Tausch, Monica Morrow, Thorsten Kühn, Walter P. Weber. Oncological Outcomes Following Omission of Axillary Lymph Node Dissection in Node Positive Patients Downstaging To Node Negative with Neoadjuvant Chemotherapy: the OPBC-04/EUBREAST-06/OMA study [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr GS4-02.
Radiographic predictors of occult intracranial involvement in olfactory neuroblastoma patients
Geltzeiler, Mathew , Ji, Keven Seung Yong , JessMace, C., Almeida, John R. de , Champagne, Pierre‐Olivier , Chan, Erik, Ciporen, Jeremy , Chaskes, Mark B., Cornell, Sarah, Drozdowski, Veronica , Fernandez‐Miranda, Juan C. , Gardner, Paul A. , Hwang, Peter H. , Kalyvas, Aristotelis , Kong, Keonho A., McMillan, Ryan A. , Patel, Chirag , Patel, Zara M. , Celda, María Peris, Sanusi, Olabisi , Thorp, Brian D. , Zadeh, Gelareh , Zenonos, Georgios A. , Zwagerman, Nathan T. , Choby, Garret , Almeida, João Paulo , McMillan, Ryan A , Nayak, Jayakar V , Patel, Zara , Pinheiro-Neto, Carlos, Snyderman, Carl H , Wang, Eric W , Hwang, Peter H , Geltzeiler, Mathew , Choby, Garret , Nayak, Jayakar V. , Pinheiro‐Neto, Carlos , Gompel, Jamie J. Van

International Forum of Allergy & Rhinology | February 26, 2023 | Volume: 13 | Issue: 10 | Pages: 1876-1888

10.1002/alr.23145 | PMID 36841933 Get It

AbstractBackgroundTraditional management of olfactory neuroblastoma (ONB) includes margin‐negative resection with removal of cribriform plate, dura, and olfactory bulb, regardless of intracranial disease. This approach may be overtreating certain patients. Our investigation examines risk factors associated with occult intracranial disease to optimize therapeutic outcomes.MethodsThis retrospective, multi‐institutional cohort study examined clinical covariates associated with occult intracranial involvement. Patient demographics, staging, Hyam's grade, and pathologic involvement of dura, olfactory bulb/tract, and brain were collected. Diagnostic imaging was reviewed. Positive and negative predictive value (NPV) were estimated along with effect size estimates. Cox hazard regression examined associations with overall survival (OS) and disease‐free survival (DFS).ResultsA total of 224 subjects with new diagnoses of ONB (2005–2021) were identified. Skull base bone involvement on computed tomography (CT) had the highest NPV for pathologic dura (88.0%), olfactory bulb (88%), and brain involvement (97.3%). Hyam's grade category was significantly associated with dural involvement (φC = 0.26; 95% confidence interval [CI]: 0.16, 0.42). Subjects without radiologic skull base involvement (n = 66) had pathologic positivity of 12.1%. Within this subgroup, Hyam's grade was clinically significant for dural positivity (φ = 0.34; 95% CI: −0.12, 0.71) with 28.6% involvement in high grade tumors. Neither clinical nor pathologic positivity of intracranial structures were associated with significantly different OS or DFS.ConclusionsBoth CT and magnetic resonance imaging (MRI) had reasonably good NPV for involvement of dura and olfactory bulb. Higher Hyam's grade was associated with dural involvement. Patients with low‐grade tumors not involving the skull base may be suitable for avoiding skull base resection; however, further investigation is warranted.
Gene expression profiles in Hispanic patients with early-onset gastric cancer.
Ju, Michelle R. , Hwang, Tae Hyun , Hong, Changjin , Karalis, John D. , Hammer, Suntrea T.G. , Porembka, Matthew R , Wang, Sam C.

Journal of Clinical Oncology | January 24, 2023 | Volume: 41 | Issue: 4_suppl | Pages: 464-464

10.1200/jco.2023.41.4_suppl.464 Get It

464 Background: A larger proportion of Hispanic gastric cancer patients are diagnosed at a young age than patients of other ethnicities. Despite diagnosis at an early age, young Hispanic patients also present more frequently with advanced disease. Whether there are molecular differences between tumors from young and old Hispanic gastric cancer patients is unknown. Methods: We performed RNA-sequencing on pre-treatment tumor samples of gastric cancer patients of self-identified Hispanic ethnicity. We stratified patients into two groups: <50 years and ≥50 years. Differentially expressed genes between groups were detected using the DESeq2 package (RStudio). We performed Gene Set Enrichment Analysis (GSEA) to identify pathways that were uniquely overexpressed in each age group. Results: 57 patients were included in our study. 23 patients were <50 years and 33 patients were ≥50 years. Comparison of the top 10% most differentially expressed genes showed no clustering based on age. However, visual inspection of the top 40 most differentially expressed genes revealed 2 distinct patterns of gene expression between age groups. GSEA revealed upregulation of DNA replication, cell cycle, and DNA repair pathways in the younger patients The tumors in younger patients also had upregulation of multiple immune activation pathways. Cancers from older patients had upregulation of programmed cell death pathways. Conclusions: Early-onset gastric cancer in Hispanic patients may represent a distinct biologic process.
Changes in CT-Based Morphological Features of the Kidney with Declining Glomerular Filtration Rate in Chronic Kidney Disease
Choi, Yoon Ho , Jo, Seongho , Lee, Ro Woon , Paek, Jin Hyuk , Kim, Byoung Je , Shin, Soo-Yong , Hwang, Seun Deuk , Lee, Seoung Woo, Song, Joon Ho , Kim, Kipyo , Shin, Soo-Yong , Song, Joon Ho , Kim, Jieun , Lee, Seoung Woo

Diagnostics | January 23, 2023 | Volume: 13 | Issue: 3 | Pages: 402

10.3390/diagnostics13030402 | PMID 36766507 Get It

Chronic kidney disease (CKD) progression involves morphological changes in the kidney, such as decreased length and thickness, with associated histopathological alterations. However, the relationship between morphological changes in the kidneys and glomerular filtration rate (GFR) has not been quantitatively and comprehensively evaluated. We evaluated the three-dimensional size and shape of the kidney using computed tomography (CT)-derived features in relation to kidney function. We included 257 patients aged ≥18 years who underwent non-contrast abdominal CT at the Inha University Hospital. The features were quantified using predefined algorithms in the pyRadiomics package after kidney segmentation. All features, except for flatness, significantly correlated with estimated GFR (eGFR). The surface-area-to-volume ratio (SVR) showed the strongest negative correlation (r = −0.75, p < 0.0001). Kidney size features, such as volume and diameter, showed moderate to high positive correlations; other morphological features showed low to moderate correlations. The calculated area under the receiver operating characteristic (ROC) curve (AUC) for different features ranged from 0.51 (for elongation) to 0.86 (for SVR) for different eGFR thresholds. Diabetes patients had weaker correlations between the studied features and eGFR and showed less bumpy surfaces in three-dimensional visualization. We identified alterations in the CKD kidney based on various three-dimensional shape and size features, with their potential diagnostic value.
TMEM161B regulates cerebral cortical gyration, Sonic Hedgehog signaling, and ciliary structure in the developing central nervous system
Akula, Shyam K. , Marciano, Jack H. , Lim, Youngshin , Exposito-Alonso, David , Hylton, Norma K. , Hwang, Grace H. , Neil, Jennifer E., Dominado, Nicole , Bunton-Stasyshyn, Rosie , Song, Janet , Talukdar, Maya , Schmid, Aloisia, Teboul, Lydia , Mo, Alisa , Finander, Benjamin , Beck, Samantha G., Yeh, Rebecca C., Otani, Aoi, Qian, Xuyu , DeGennaro, Ellen M. , Alkuraya, Fowzan S. , Maddirevula, Sateesh , Cascino, Gregory D. , Network, Undiagnosed Diseases, Burrage, Lindsay C. , Rosenfield, Jill A., Ketkar, Shamika , Clark, Gary, Bacino, Carlos A. , Lewis, Richard A. , Segal, Rosalind A. , Bazán, J. Fernando , Smith, K. A. , Golden, Jeffrey A. , Cho, Ginam , Walsh, Christopher A. , Alejandro, Mercedes E., Ashley, Euan A. , Baker, Eva H. , Balasubramanyam, Ashok , Barseghyan, Hayk , Batzli, Gabriel F., Bernstein, Jonathan A. , Bican, Anna, Bick, David , Birch, Camille L., Boone, Braden, Bostwick, Bret L. , Briere, Lauren C. , Brokamp, Elly , Brush, Matthew , Chen, Shan , Coakley, Terra R., Cobban, Laurel A., Colley, Heather A., Cooper, Cynthia M. , Craigen, William J., D’Souza, Precilla , Davids, Mariska, Davidson, Jean M. , Dayal, Jyoti G. , Dell’Angelica, Esteban C., Dhar, Shweta U. , Dipple, Katrina M. , Dorrani, Naghmeh, Dorset, Daniel C., Douglas, Jessica, Draper, David D., Dries, Annika M., Eckstein, David J. , Emrick, Lisa , Eng, Christine M. , Enns, Gregory M. , Eskin, Ascia , Esteves, Cecilia, Estwick, Tyra, Fernández, Liliana, Fogel, Brent L. , Friedman, Noah D., Gahl, William A. , Godfrey, Rena A., Goldstein, David B. , Gould, Sarah E., Groden, Catherine, Hamid, Rizwan , Hanchard, Neil A. , High, Frances A. , Hom, Jason , Howerton, Ellen M. , Jamal, Fariha , Jiang, Yong‐hui , Johnston, Jean M., Karaviti, Lefkothea , Kelley, Emily G., Koeller, David M. , Kohane, Isaac S. , Kohler, Jennefer N., Korrick, Susan , Kozuira, Mary, Krasnewich, Donna M., Krier, Joel B. , Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly , Lee, Brendan , Lee, Hane , Lewis, Richard A., Loscalzo, Joseph, Maas, Richard L., MacRae, Calum A. , Maduro, Valerie V. , Majcherska, Marta M., Malicdan, May Christine V. , Mamounas, Laura A., Manolio, Teri A. , Markello, Thomas C. , Martín, Martín G., Marwaha, Shruti , May, Thomas , McConkie‐Rosell, Allyn , McCormack, Colleen E., McCray, Alexa T. , Merker, Jason D. , Moretti, Paolo , Morimoto, Marie , Murdock, David R. , Muzny, Donna M., Nehrebecky, Michele, Nelson, Stan F., Newberry, J. Scott, Newman, John H. , Nicholas, Sarah K. , Novacic, Donna, Orengo, James P. , Pallais, J. Carl , Palmer, Christina G.S. , Papp, Jeanette C. , Parker, Neil H., Peña, Loren D.M. , Phillips, John A., Potocki, Lorraine , Pusey, Barbara N., Renteria, Genecee, Rives, Lynette, Robertson, Amy K., Rodan, Lance H. , Sampson, Jacinda B. , Samson, Susan L. , Schoch, Kelly, Shakachite, Lisa, Sharma, Prashant , Shashi, Vandana , Signer, Rebecca , Silverman, Edwin K. , Smith, Kevin S., Spillmann, Rebecca C. , Stoler, Joan M. , Sullivan, Jennifer A. , Tan, Queenie K.‐G., Tan, Wen-Haan, Toro, Camilo , Tran, Alyssa A., Urv, Tiina K. , Vogel, Tiphanie P. , Waggott, Daryl, Wahl, Colleen E., Walker, Melissa , Walley, Nicole M., Wan, Jijun , Ward, Patricia A., Westerfield, Monte, Wise, Anastasia L., Wolfe, Lynne A. , Yang, Yaping , Yoon, Amanda J., Yu, Guoyun, Zastrow, Diane B. , Zhao, Chunli , Zheng, Allison, Bunton-Stasyshyn, Rosie K , DeGennaro, Ellen M , Cascino, Gregory D , Giannini, Caterina , Burrage, Lindsay C , Rosenfield, Jill A , Bacino, Carlos , Lewis, Richard A , Segal, Rosalind A , Bazan, J Fernando , Smith, Kelly A , Golden, Jeffrey A , Cho, Ginam , Walsh, Christopher A , Alkuraya, Fowzan S , Akula, Shyam K , Shin, Taehwan , Giannini, Caterina , Network, Undiagnosed Diseases, Adams, David R. , Aday, Aaron W. , Allard, Patrick , Azamian, Mahshid S. , Beggs, Alan H. , Behnam, Babak , Bellen, Hugo J. , Berry, Gerard T. , Bonner, Devon E. , Brown, Donna M. , Burke, Elizabeth A. , Butte, Manish J. , Cogan, Joy D. , Cope, Heidi , D’Souza, Precilla , Douine, Emilie D. , Ferreira, Carlos R , Fieg, Elizabeth L. , Fisher, Paul Graham , Goldman, Alica M. , Gourdine, Jean-Philippe F. , Gropman, Andrea L , Haendel, Melissa , Holm, Ingrid A. , Huang, Yong , Jones, Angela , Kyle, Jennifer E , Lalani, Seema R , Levy, Shawn , Lewis, Richard A., Loo, Sandra K. , Macnamara, Ellen F. , Marom, Ronit , Martínez-Agosto, Julián A. , May, Thomas, Metz, Thomas , Might, Matthew , Mochida, Ganeshwaran H. , Mulvihill, John Joseph , Murphy, Jennifer L. , Muzny, Donna M. , Orange, Jordan S. , Phillips, John A., Posey, Jennifer E , Postlethwait, John H. , Reuter, Chloe M. , Rosenfeld, Jill A. , Scott, Daryl A , Sinsheimer, Janet S. , Stong, Nicholas , Sweetser, David A , Tifft, Cynthia , Vilain, Eric J. N. , Walley, Nicole M., Wangler, Michael F , Waters, Katrina M. , Webb‐Robertson, Bobbie‐Jo , Wheeler, Matthew T , Worthey, Elizabeth A. , Yamamoto, Shinya , Yang, John Jeongseok

Proceedings of the National Academy of Sciences | January 20, 2023 | Volume: 120 | Issue: 4 | Pages: No page available

10.1073/pnas.2209964120 | PMID 36669111 Get It

Sonic hedgehog signaling regulates processes of embryonic development across multiple tissues, yet factors regulating context-specific Shh signaling remain poorly understood. Exome sequencing of families with polymicrogyria (disordered cortical folding) revealed multiple individuals with biallelic deleterious variants in TMEM161B , which encodes a multi-pass transmembrane protein of unknown function. Tmem161b null mice demonstrated holoprosencephaly, craniofacial midline defects, eye defects, and spinal cord patterning changes consistent with impaired Shh signaling, but were without limb defects, suggesting a CNS-specific role of Tmem161b. Tmem161b depletion impaired the response to Smoothened activation in vitro and disrupted cortical histogenesis in vivo in both mouse and ferret models, including leading to abnormal gyration in the ferret model. Tmem161b localizes non-exclusively to the primary cilium, and scanning electron microscopy revealed shortened, dysmorphic, and ballooned ventricular zone cilia in the Tmem161b null mouse, suggesting that the Shh-related phenotypes may reflect ciliary dysfunction. Our data identify TMEM161B as a regulator of cerebral cortical gyration, as involved in primary ciliary structure, as a regulator of Shh signaling, and further implicate Shh signaling in human gyral development.
Diagnosis of Alzheimer’s disease and tauopathies on whole slide histopathology images using a weakly supervised deep learning algorithm
Yao, Gary, Martin, Nicholas B. , Castanedes‐Casey, Monica , Hwang, Tae Hyun , Koga, Shunsuke , Koga, Shunsuke , Kim, Minji , Sekiya, Hiroaki , Dickson, Dennis W.

No container title available | January 16, 2023 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.21203/rs.3.rs-2459626/v2 Get It

Abstract Neuropathological assessment at autopsy is the gold standard for diagnosing neurodegenerative disorders. We aimed to develop a pipeline for diagnosing Alzheimer's disease and other tauopathies, including corticobasal degeneration, globular glial tauopathy, Pick’s disease, and progressive supranuclear palsy. We used deep learning (DL)-based approach called clustering-constrained-attention multiple instance learning (CLAM) on whole slide images (WSIs) of tau immunohistochemistry in three brain regions from 120 patients. We also augmented gradient-weighted class activation mapping (Grad-CAM) to the model for visualizing cellular-level evidence in the model’s decisions. The model using the sections of cingulate and superior frontal gyri achieved the highest area under the curve (0.970±0.037) and diagnostic accuracy (0.873±0.087). Grad-CAM showed the highest attention in known pathognomonic tau lesions for each disease (e.g., Pick bodies for Pick’s disease). Our findings supported the feasibility of the DL-based approach for the classification task on WSIs, which encouraged further investigation, especially focusing on clinicopathological correlation studies.
Peritoneal metastases from primary appendiceal and colorectal carcinomas demonstrate distinct molecular identities on comprehensive tumor analysis
Fleming, Andrew M. , Deschner, Benjamin W. , Williard, Forrest W., Xiu, Joanne , Somer, Bradley G. , Yakoub, Danny , Tsao, Miriam , Glazer, Evan S. , Dickson, Paxton V. , Shibata, David , Hwang, Jimmy J., Shields, Anthony F. , Lenz, Heinz‐Josef , Deneve, Jeremiah L. , Glazer, Evan S , Dickson, Paxton V , Deneve, Jeremiah L , Reiter, Audra , Drake, Justin A. , Vanderwalde, Ari M. , Philip, Philip A. , Marshall, John L , Korn, Wolfgang Michael

Journal of Surgical Oncology | January 11, 2023 | Volume: 127 | Issue: 5 | Pages: 815-822

10.1002/jso.27198 | PMID 36629137 Get It

AbstractBackground and ObjectivesPublished data comparing peritoneal metastases from appendiceal cancers (pAC) and colorectal cancers (pCRC) remain sparse. We compared pAC and pCRC using comprehensive tumor profiling (CTP).MethodsCTP was performed, including next‐generation sequencing and analysis of copy number variation (CNV), microsatellite instability (MSI) and tumor mutational burden (TMB).ResultsOne hundred thirty‐six pAC and 348 pCRC samples underwent CTP. The cohorts' age and gender were similar. pCRC demonstrated increased pathogenic variants (PATHs) in APC (48% vs. 3%, p < 0.01), ARID1A (12% vs. 2%, p < 0.01), BRAF (12% vs. 2%, p < 0.01), FBXW7 (7% vs. 2%, p < 0.01), KRAS (52% vs. 41%, p < 0.05), PIK3CA (15% vs. 2%, p < 0.01), and TP53 (53% vs. 23%, p < 0.01), and decreased PATHs in GNAS (8% vs. 31%, p < 0.01). There was no difference in CNV, fusion rate, or MSI. Median TMB was higher in pCRC (5.8 vs. 5.0 mutations per megabase, p = 0.0007). Rates of TMB‐high tumors were similar (pAC 2.1% vs. pCRC 9.0%, p = 0.1957). pCRC had significantly more TMB‐high tumors at lower thresholds.ConclusionsDespite a reduced overall TMB, pAC demonstrated mutations distinct from those seen in pCRC. These may serve as discrete biomarkers for future study.