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Matt GY, Sioson E, Shelton K, Wang J, Lu C, Zaldivar Peraza A, Gangwani K, Paul R, Reilly C, Acić A, Liu Q, Sandor SR, McLeod C, Patel J, Wang F, Im C, Wang Z, Sapkota Y, Wilson CL, Bhakta N, Ness KK, Armstrong GT, Hudson MM, Robison LL, Zhang J, Yasui Y, Zhou X. St. Jude Survivorship Portal: sharing and analyzing large clinical and genomic datasets from pediatric cancer survivors. Cancer Discov 2024:742905. [PMID: 38593228 DOI: 10.1158/2159-8290.cd-23-1441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/08/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Childhood cancer survivorship studies generate comprehensive datasets comprising demographic, diagnosis, treatment, outcome, and genomic data from survivors. To broadly share this data, we created the St. Jude Survivorship Portal (https://survivorship.stjude.cloud), the first data portal for sharing, analyzing, and visualizing pediatric cancer survivorship data. Over 1,600 phenotypic variables and 400 million genetic variants from over 7,700 childhood cancer survivors can be explored on this free, open-access portal. Summary statistics of variables are computed on-the-fly and visualized through interactive and customizable charts. Survivor cohorts can be customized and/or divided into groups for comparative analysis. Users can also seamlessly perform cumulative incidence and regression analyses on the stored survivorship data. Using the portal, we explored the ototoxic effects of platinum-based chemotherapy, uncovered a novel association between mental health, age, and limb amputation, and discovered a novel haplotype in MAGI3 strongly associated with cardiomyopathy specifically in survivors of African ancestry.
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Affiliation(s)
- Gavriel Y Matt
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Edgar Sioson
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Kyla Shelton
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jian Wang
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Congyu Lu
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | - Robin Paul
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Colleen Reilly
- St. Jude Children's Research Hospital, Memphis, United States
| | - Aleksandar Acić
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Qi Liu
- University of Alberta, Edmonton, Alberta, Canada
| | | | - Clay McLeod
- St. Jude Children's Research Hospital, Memphis, United States
| | - Jaimin Patel
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Fan Wang
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Cindy Im
- University of Minnesota, Minneapolis, MN, United States
| | - Zhaoming Wang
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Yadav Sapkota
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Carmen L Wilson
- St. Jude Children's Research Hospital, Memphis, TENNESSEE, United States
| | - Nickhill Bhakta
- St. Jude Children's Research Hospital, Memphis, United States
| | - Kirsten K Ness
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | - Melissa M Hudson
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Leslie L Robison
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jinghui Zhang
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Yutaka Yasui
- St. Jude Children's Research Hospital, Memphis, United States
| | - Xin Zhou
- St. Jude Children's Research Hospital, memphis, United States
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Iacobucci I, Zeng AGX, Gao Q, Garcia-Prat L, Baviskar P, Shah S, Murison A, Voisin V, Chan-Seng-Yue M, Cheng C, Qu C, Bailey C, Lear M, Witkowski MT, Zhou X, Peraza AZ, Gangwani K, Advani AS, Luger SM, Litzow MR, Rowe JM, Paietta EM, Stock W, Dick JE, Mullighan CG. SINGLE CELL DISSECTION OF DEVELOPMENTAL ORIGINS AND TRANSCRIPTIONAL HETEROGENEITY IN B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA. bioRxiv 2023:2023.12.04.569954. [PMID: 38106088 PMCID: PMC10723356 DOI: 10.1101/2023.12.04.569954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Sequencing of bulk tumor populations has improved genetic classification and risk assessment of B-ALL, but does not directly examine intratumor heterogeneity or infer leukemia cellular origins. We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) and compared them to a reference map of normal human B-cell development established using both functional and molecular assays. Intra-sample heterogeneity was driven by cell cycle, metabolism, differentiation, and inflammation transcriptional programs. By inference of B lineage developmental state composition, nearly all samples possessed a high abundance of pro-B cells, with variation between samples mainly driven by sub-populations. However, ZNF384- r and DUX4- r B-ALL showed composition enrichment of hematopoietic stem cells, BCR::ABL1 and KMT2A -r ALL of Early Lymphoid progenitors, MEF2D -r and TCF3::PBX1 of Pre-B cells. Enrichment of Early Lymphoid progenitors correlated with high-risk clinical features. Understanding variation in transcriptional programs and developmental states of B-ALL by scRNA-seq refines existing clinical and genomic classifications and improves prediction of treatment outcome.
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Waghmare I, Gangwani K, Rai A, Singh A, Kango-Singh M. A Tumour-Specific Molecular Network Promotes Tumour Growth in Drosophila by Enforcing a JNK-YKI Feedforward Loop. bioRxiv 2023:2023.10.18.561369. [PMID: 37904920 PMCID: PMC10614921 DOI: 10.1101/2023.10.18.561369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Cancer cells expand rapidly in response to altered intercellular and signalling interactions to achieve hallmarks of cancer. Impaired cell polarity combined with activated oncogenes is known to promote several hallmarks of cancer e.g., activating invasion by increased activity of Jun N-terminal kinase (JNK), and sustained proliferative signalling by increased activity of Hippo effector Yorkie (Yki). Thus, JNK, Yki, and their downstream transcription factors have emerged as synergistic drivers of tumour growth through pro-tumour signalling and intercellular interactions like cell-competition. However, little is known about the signals that converge onto JNK and Yki in tumour cells that enable the tumour cells to achieve hallmarks of cancer. Here, using mosaic models of cooperative oncogenesis ( Ras V12 , scrib - ) in Drosophila , we show that Ras V12 , scrib - tumour cells grow by activation of a previously unidentified network comprising Wingless (Wg), Dronc, JNK and Yki. We show that Ras V12 , scrib - cells show increased Wg, Dronc, JNK, and Yki signalling, and all of these signals are required for the growth of Ras V12 , scrib - tumours. We report that Wg and Dronc converge onto a JNK-Yki self-reinforcing positive feedback signal-amplification loop that promotes tumour growth. We found that Wg-Dronc-Yki-JNK molecular network is specifically activated in polarity-impaired tumour cells and not in normal cells where apical basal polarity is intact. Our findings suggest that identification of molecular networks may provide significant insights about the key biologically meaningful changes in signalling pathways, and paradoxical signals that promote Tumourigenesis.
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Bautista C, Alfuraiji N, Drangowska-Way A, Gangwani K, de Flamingh A, Bourne PE. Ten simple rules for improving communication among scientists. PLoS Comput Biol 2022; 18:e1010130. [PMID: 35737640 PMCID: PMC9223317 DOI: 10.1371/journal.pcbi.1010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Communication is a fundamental part of scientific development and methodology. With the advancement of the internet and social networks, communication has become rapid and sometimes overwhelming, especially in science. It is important to provide scientists with useful, effective, and dynamic tools to establish and build a fluid communication framework that allows for scientific advancement. Therefore, in this article, we present advice and recommendations that can help promote and improve science communication while respecting an adequate balance in the degree of commitment toward collaborative work. We have developed 10 rules shown in increasing order of commitment that are grouped into 3 key categories: (1) speak (based on active participation); (2) join (based on joining scientific groups); and (3) assess (based on the analysis and retrospective consideration of the weaknesses and strengths). We include examples and resources that provide actionable strategies for involvement and engagement with science communication, from basic steps to more advanced, introspective, and long-term commitments. Overall, we aim to help spread science from within and encourage and engage scientists to become involved in science communication effectively and dynamically.
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Affiliation(s)
- Carla Bautista
- Early Career Scientist Communication and Outreach Subcommittee, Genetics Society of America, Rockville, Maryland, United States of America
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de Recherche sur la Fonction, la Structure et L’ingénierie des Protéines (PROTEO), Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Narjes Alfuraiji
- Early Career Scientist Communication and Outreach Subcommittee, Genetics Society of America, Rockville, Maryland, United States of America
- Department of Pharmacology, College of Medicine, University of Kerbala, Kerbala, Iraq
| | - Anna Drangowska-Way
- Early Career Scientist Communication and Outreach Subcommittee, Genetics Society of America, Rockville, Maryland, United States of America
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Karishma Gangwani
- Early Career Scientist Communication and Outreach Subcommittee, Genetics Society of America, Rockville, Maryland, United States of America
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Alida de Flamingh
- Early Career Scientist Communication and Outreach Subcommittee, Genetics Society of America, Rockville, Maryland, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Philip E. Bourne
- School of Data Science, University of Virginia, Charlottesville, Virginia, United States of America
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Gangwani K, Snigdha K, Kango-Singh M. Tep1 Regulates Yki Activity in Neural Stem Cells in Drosophila Glioma Model. Front Cell Dev Biol 2020; 8:306. [PMID: 32457905 PMCID: PMC7225285 DOI: 10.3389/fcell.2020.00306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma Multiforme (GBM) is the most common form of malignant brain tumor with poor prognosis. Amplification of Epidermal Growth Factor Receptor (EGFR), and mutations leading to activation of Phosphatidyl-Inositol-3 Kinase (PI3K) pathway are commonly associated with GBM. Using a previously published Drosophila glioma model generated by coactivation of PI3K and EGFR pathways [by downregulation of Pten and overexpression of oncogenic Ras] in glial cells, we showed that the Drosophila Tep1 gene (ortholog of human CD109) regulates Yki (the Drosophila ortholog of human YAP/TAZ) via an evolutionarily conserved mechanism. Oncogenic signaling by the YAP/TAZ pathway occurs in cells that acquire CD109 expression in response to the inflammatory environment induced by radiation in clinically relevant models. Further, downregulation of Tep1 caused a reduction in Yki activity and reduced glioma growth. A key function of Yki in larval CNS is stem cell renewal and formation of neuroblasts. Other reports suggest different upstream regulators of Yki activity in the optic lobe versus the central brain regions of the larval CNS. We hypothesized that Tep1 interacts with the Hippo pathway effector Yki to regulate neuroblast numbers. We tested if Tep1 acts through Yki to affect glioma growth, and if in normal cells Tep1 affects neuroblast number and proliferation. Our data suggests that Tep1 affects Yki mediated stem cell renewal in glioma, as reduction of Tep significantly decreases the number of neuroblasts in glioma. Thus, we identify Tep1-Yki interaction in the larval CNS that plays a key role in glioma growth and progression.
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Affiliation(s)
- Karishma Gangwani
- Department of Biology, University of Dayton, Dayton, OH, United States
| | - Kirti Snigdha
- Department of Biology, University of Dayton, Dayton, OH, United States
| | - Madhuri Kango-Singh
- Department of Biology, University of Dayton, Dayton, OH, United States
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, United States
- Premedical Programs, University of Dayton, Dayton, OH, United States
- Integrated Science and Engineering Center (ISE), University of Dayton, Dayton, OH, United States
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Bundale S, Begde D, Pillai D, Gangwani K, Nashikkar N, Kadam T, Upadhyay A. Novel aromatic polyketides from soil Streptomyces spp.: purification, characterization and bioactivity studies. World J Microbiol Biotechnol 2018; 34:67. [DOI: 10.1007/s11274-018-2448-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/14/2018] [Indexed: 11/24/2022]
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