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Yu H. Reproductive toxicity and gene expression alterations in aquatic environments: Expanding the insights of the recent guppy study on PFAS exposure. ENVIRONMENT INTERNATIONAL 2024; 190:108923. [PMID: 39137686 DOI: 10.1016/j.envint.2024.108923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024]
Affiliation(s)
- Haoxuan Yu
- Water Engineering Discipline, Department of Civil Engineering, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia; Monash Climate-Resilient Infrastructure Research Hub (M-CRInfra), School of Engineering, Monash University Malaysia, 47500, Bandar Sunway, Malaysia.
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2
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Ishikawa A, Fukui T, Kido A, Katsuya N, Kuraoka K, Uraoka N, Suzuki T, Oka S, Kotachi T, Ashktorab H, Smoot D, Yasui W. Discovering cancer stem-like molecule, nuclear factor I X, using spatial transcriptome in gastric cancer. Cancer Sci 2024. [PMID: 39021298 DOI: 10.1111/cas.16288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024] Open
Abstract
Gastric cancer (GC) is characterized by significant intratumoral heterogeneity, and stem cells are promising therapeutic targets. Despite advancements in spatial transcriptome analyses, unexplored targets for addressing cancer stemness remain unknown. This study aimed to identify Nuclear Factor IX (NFIX) as a critical regulator of cancer stemness in GC and evaluate its clinicopathological significance and function. Spatial transcriptome analysis of GC was conducted. The correlation between NFIX expression, clinicopathological factors, and prognosis was assessed using immunostaining in 127 GC cases. Functional analyses of cancer cell lines validated these findings. Spatial transcriptome analysis stratified GC tissues based on genetic profiles, identified CSC-like cells, and further refined the classification to identify and highlight the significance of NFIX, as validated by Monocle 3 and CytoTRACE analyses. Knockdown experiments in cancer cell lines have demonstrated the involvement of NFIX in cancer cell proliferation and kinase activity. This study underscores the role of spatial transcriptome analysis in refining GC tissue classification and identifying therapeutic targets, highlighting NFIX as a pivotal factor. NFIX expression is correlated with poor prognosis and drives GC progression, suggesting its potential as a novel therapeutic target for personalized GC therapies.
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Affiliation(s)
- Akira Ishikawa
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takafumi Fukui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Aya Kido
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Narutaka Katsuya
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuya Kuraoka
- Department of Diagnostic Pathology, National Hospital Organization (NHO), Kure Medical Center and Chugoku Cancer Center, Kure, Hiroshima, Japan
| | - Naohiro Uraoka
- Department of Pathology, Kure Kyosai Hospital, Federation of National Public Services and Affiliated Personnel Mutual Aid Associations, Kure, Japan
| | - Takahisa Suzuki
- Department of Surgery, National Hospital Organization (NHO), Kure Medical Center and Chugoku Cancer Center, Kure, Hiroshima, Japan
| | - Shiro Oka
- Department of Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takahiro Kotachi
- Department of Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Wataru Yasui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Division of Pathology, Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
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3
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Watanabe R, Miura N, Kurata M, Kitazawa R, Kikugawa T, Saika T. Unveiling the Genomic Landscape of Intraductal Carcinoma of the Prostate Using Spatial Gene Expression Analysis. Int J Mol Sci 2024; 25:4818. [PMID: 38732035 PMCID: PMC11083946 DOI: 10.3390/ijms25094818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Intraductal carcinoma of the prostate (IDCP) has recently attracted increasing interest owing to its unfavorable prognoses. To effectively identify the IDCP-specific gene expression profile, we took a novel approach of characterizing a typical IDCP case using spatial gene expression analysis. A formalin-fixed, paraffin-embedded sample was subjected to Visium CytAssist Spatial Gene Expression analysis. IDCP within invasive prostate cancer sites was recognized as a distinct cluster separate from other invasive cancer clusters. Highly expressed genes defining the IDCP cluster, such as MUC6, MYO16, NPY, and KLK12, reflected the aggressive nature of high-grade prostate cancer. IDCP sites also showed increased hypoxia markers HIF1A, BNIP3L, PDK1, and POGLUT1; decreased fibroblast markers COL1A2, DCN, and LUM; and decreased immune cell markers CCR5 and FCGR3A. Overall, these findings indicate that the hypoxic tumor microenvironment and reduced recruitment of fibroblasts and immune cells, which reflect morphological features of IDCP, may influence the aggressiveness of high-grade prostate cancer.
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Affiliation(s)
- Ryuta Watanabe
- Department of Urology, Ehime University Graduate School of Medicine, Toon 791-0295, Japan; (N.M.); (T.K.); (T.S.)
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noriyoshi Miura
- Department of Urology, Ehime University Graduate School of Medicine, Toon 791-0295, Japan; (N.M.); (T.K.); (T.S.)
| | - Mie Kurata
- Department of Analytical Pathology, Ehime University Graduate School of Medicine, Toon 791-0295, Japan;
- Division of Pathology, Proteo-Science Center, Ehime University, Toon 791-0295, Japan
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital, Toon 791-0295, Japan;
| | - Tadahiko Kikugawa
- Department of Urology, Ehime University Graduate School of Medicine, Toon 791-0295, Japan; (N.M.); (T.K.); (T.S.)
| | - Takashi Saika
- Department of Urology, Ehime University Graduate School of Medicine, Toon 791-0295, Japan; (N.M.); (T.K.); (T.S.)
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Chidambaram A, Prabhakaran R, Sivasamy S, Kanagasabai T, Thekkumalai M, Singh A, Tyagi MS, Dhandayuthapani S. Male Breast Cancer: Current Scenario and Future Perspectives. Technol Cancer Res Treat 2024; 23:15330338241261836. [PMID: 39043043 PMCID: PMC11271170 DOI: 10.1177/15330338241261836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 05/06/2024] [Accepted: 05/28/2024] [Indexed: 07/25/2024] Open
Abstract
Male breast cancer (MBC), one of the rare types of cancer among men where the global incidence rate is 1.8% of all breast cancers cases with a yearly increase in a pace of 1.1%. Since the last 10 years, the incidence has been increased from 7.2% to 10.3% and the mortality rate was decreased from 11% to 3.8%. Nevertheless, the rate of diagnoses has been expected to be around 2.6% in the near future, still there is a great lack in studies to characterize the MBC including the developed countries. Based on our search, it is evidenced from the literature that the number of risk factors for the cause of MBC are significant, which includes the increase in age, family genetic history, mutations in specific genes due to various environmental impacts, hormonal imbalance and unregulated expression receptors for specific hormones of high levels of estrogen or androgen receptors compared to females. MBCs are broadly classified into ductal and lobular carcinomas with further sub-types, with some of the symptoms including a lump or swelling in the breast, redness of flaky skin in the breast, irritation and nipple discharge that is similar to the female breast cancer (FBC). The most common diagnostic tools currently in use are the ultrasound guided sonography, mammography, and biopsies. Treatment modalities for MBC include surgery, radiotherapy, chemotherapy, hormonal therapy, and targeted therapies. However, the guidelines followed for the diagnosis and treatment modalities of MBC are mostly based on FBC that is due to the lack of prospective studies related to MBC. However, there are distinct clinical and molecular features of MBC, it is a need to develop different clinical methods with more multinational approaches to help oncologist to improve care for MBC patients.
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Affiliation(s)
- Anitha Chidambaram
- Department of Biochemistry, PRIST Deemed to be University, Thanjavur, TN, India
| | - Rajkumar Prabhakaran
- Central Research Facility, Santosh Deemed to be University, Ghaziabad, UP, India
| | - Sivabalan Sivasamy
- Central Research Facility, Santosh Deemed to be University, Ghaziabad, UP, India
| | - Thanigaivelan Kanagasabai
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN, USA
| | - Malarvili Thekkumalai
- Department of Biochemistry, Center for Distance Education, Bharathidasan University, Tiruchirappalli, TN, India
| | - Ankit Singh
- Department of Community Medicine, United Institute of Medical Sciences, Prayagraj, UP, India
| | - Mayurika S. Tyagi
- Department of Immuno Hematology and Blood Transfusion, Santosh Deemed to be University, Ghaziabad, UP, India
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5
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Suzuki A, Nojima S, Tahara S, Motooka D, Kohara M, Okuzaki D, Hirokawa M, Morii E. Identification of invasive subpopulations using spatial transcriptome analysis in thyroid follicular tumors. J Pathol Transl Med 2024; 58:22-28. [PMID: 38229431 DOI: 10.4132/jptm.2023.11.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Follicular tumors include follicular thyroid adenomas and carcinomas; however, it is difficult to distinguish between the two when the cytology or biopsy material is obtained from a portion of the tumor. The presence or absence of invasion in the resected material is used to differentiate between adenomas and carcinomas, which often results in the unnecessary removal of the adenomas. If nodules that may be follicular thyroid carcinomas are identified preoperatively, active surveillance of other nodules as adenomas is possible, which reduces the risk of surgical complications and the expenses incurred during medical treatment. Therefore, we aimed to identify biomarkers in the invasive subpopulation of follicular tumor cells. METHODS We performed a spatial transcriptome analysis of a case of follicular thyroid carcinoma and examined the dynamics of CD74 expression in 36 cases. RESULTS We identified a subpopulation in a region close to the invasive area, and this subpopulation expressed high levels of CD74. Immunohistochemically, CD74 was highly expressed in the invasive and peripheral areas of the tumor. CONCLUSIONS Although high CD74 expression has been reported in papillary and anaplastic thyroid carcinomas, it has not been analyzed in follicular thyroid carcinomas. Furthermore, the heterogeneity of CD74 expression in thyroid tumors has not yet been reported. The CD74-positive subpopulation identified in this study may be useful in predicting invasion of follicular thyroid carcinomas.
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Affiliation(s)
- Ayana Suzuki
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, Kobe, Hyogo, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masaharu Kohara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Mitsuyoshi Hirokawa
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, Kobe, Hyogo, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
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6
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Dutta S, Bhattacharya S, Harris H, Islam R, Bodas S, Polavaram N, Mishra J, Das D, Seshacharyulu P, Kalluchi A, Pal A, Kohli M, Lele S, Muders M, Batra S, Ghosh P, Datta K, Rowley M. Understanding the role of Pax5 in development of taxane-resistant neuroendocrine like prostate cancers. RESEARCH SQUARE 2023:rs.3.rs-3464475. [PMID: 38168280 PMCID: PMC10760218 DOI: 10.21203/rs.3.rs-3464475/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Resistance to the current Androgen Receptor Signaling Inhibitor (ARSI) therapies has led to higher incidences of therapy-induced neuroendocrine-like prostate cancer (t-NEPC). This highly aggressive subtype with predominant small cell-like characteristics is resistant to taxane chemotherapies and has a dismal overall survival. t-NEPCs are mostly treated with platinum-based drugs with a combination of etoposide or taxane and have less selectivity and high systemic toxicity, which often limit their clinical potential. During t-NEPC transformation, adenocarcinomas lose their luminal features and adopt neuro-basal characteristics. Whether the adaptive neuronal characteristics of t-NEPC are responsible for such taxane resistance remains unknown. Pathway analysis from patient gene-expression databases indicates that t-NEPC upregulates various neuronal pathways associated with enhanced cellular networks. To identify transcription factor(s) (TF) that could be important for promoting the gene expression for neuronal characters in t-NEPC, we performed ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq in our NE-like cell line models and analyzed the promoters of transcriptionally active and significantly enriched neuroendocrine-like (NE-like) cancer-specific genes. Our results indicate that Pax5 could be an important transcription factor for neuronal gene expression and specific to t-NEPC. Pathway analysis revealed that Pax5 expression is involved in axonal guidance, neurotransmitter regulation, and neuronal adhesion, which are critical for strong cellular communications. Further results suggest that depletion of Pax5 disrupts cellular interaction in NE-like cells and reduces surface growth factor receptor activation, thereby, sensitizing them to taxane therapies. Moreover, t-NEPC specific hydroxymethylation of Pax5 promoter CpG islands favors Pbx1 binding to induce Pax5 expression. Based on our study, we concluded that continuous exposure to ARSI therapies leads to epigenetic modifications and Pax5 activation in t-NEPC, which promotes the expression of genes necessary to adopt taxane-resistant NE-like cancer. Thus, targeting the Pax5 axis can be beneficial for reverting their taxane sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Muders
- Rudolf Becker Laboratory for Prostate Cancer Research, Center of Pathology, University of Bonn Medical Center
| | - Surinder Batra
- University of Nebraska Medical Center, Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases
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7
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Logotheti S, Papadaki E, Zolota V, Logothetis C, Vrahatis AG, Soundararajan R, Tzelepi V. Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics. Cancers (Basel) 2023; 15:4357. [PMID: 37686633 PMCID: PMC10486655 DOI: 10.3390/cancers15174357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer (PCa), the most frequent and second most lethal cancer type in men in developed countries, is a highly heterogeneous disease. PCa heterogeneity, therapy resistance, stemness, and lethal progression have been attributed to lineage plasticity, which refers to the ability of neoplastic cells to undergo phenotypic changes under microenvironmental pressures by switching between developmental cell states. What remains to be elucidated is how to identify measurements of lineage plasticity, how to implement them to inform preclinical and clinical research, and, further, how to classify patients and inform therapeutic strategies in the clinic. Recent research has highlighted the crucial role of next-generation sequencing technologies in identifying potential biomarkers associated with lineage plasticity. Here, we review the genomic, transcriptomic, and epigenetic events that have been described in PCa and highlight those with significance for lineage plasticity. We further focus on their relevance in PCa research and their benefits in PCa patient classification. Finally, we explore ways in which bioinformatic analyses can be used to determine lineage plasticity based on large omics analyses and algorithms that can shed light on upstream and downstream events. Most importantly, an integrated multiomics approach may soon allow for the identification of a lineage plasticity signature, which would revolutionize the molecular classification of PCa patients.
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Affiliation(s)
- Souzana Logotheti
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Eugenia Papadaki
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
- Department of Informatics, Ionian University, 49100 Corfu, Greece;
| | - Vasiliki Zolota
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | | | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vasiliki Tzelepi
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
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Krieger KL, Mann EK, Lee KJ, Bolterstein E, Jebakumar D, Ittmann MM, Dal Zotto VL, Shaban M, Sreekumar A, Gassman NR. Spatial mapping of the DNA adducts in cancer. DNA Repair (Amst) 2023; 128:103529. [PMID: 37390674 PMCID: PMC10330576 DOI: 10.1016/j.dnarep.2023.103529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
DNA adducts and strand breaks are induced by various exogenous and endogenous agents. Accumulation of DNA damage is implicated in many disease processes, including cancer, aging, and neurodegeneration. The continuous acquisition of DNA damage from exogenous and endogenous stressors coupled with defects in DNA repair pathways contribute to the accumulation of DNA damage within the genome and genomic instability. While mutational burden offers some insight into the level of DNA damage a cell may have experienced and subsequently repaired, it does not quantify DNA adducts and strand breaks. Mutational burden also infers the identity of the DNA damage. With advances in DNA adduct detection and quantification methods, there is an opportunity to identify DNA adducts driving mutagenesis and correlate with a known exposome. However, most DNA adduct detection methods require isolation or separation of the DNA and its adducts from the context of the nuclei. Mass spectrometry, comet assays, and other techniques precisely quantify lesion types but lose the nuclear context and even tissue context of the DNA damage. The growth in spatial analysis technologies offers a novel opportunity to leverage DNA damage detection with nuclear and tissue context. However, we lack a wealth of techniques capable of detecting DNA damage in situ. Here, we review the limited existing in situ DNA damage detection methods and examine their potential to offer spatial analysis of DNA adducts in tumors or other tissues. We also offer a perspective on the need for spatial analysis of DNA damage in situ and highlight Repair Assisted Damage Detection (RADD) as an in situ DNA adduct technique with the potential to integrate with spatial analysis and the challenges to be addressed.
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Affiliation(s)
- Kimiko L Krieger
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
| | - Elise K Mann
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Kevin J Lee
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Elyse Bolterstein
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Deborah Jebakumar
- Department of Anatomic Pathology, Baylor Scott & White Medical Center, Temple, TX 76508, USA; Texas A&M College of Medicine, Temple, TX 76508, USA
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Human Tissue Acquisition & Pathology Shared Resource, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valeria L Dal Zotto
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Mohamed Shaban
- Department of Electrical and Computer Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natalie R Gassman
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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