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Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism.

bioRxiv : the preprint server for biology

Policard M, Jain S, Rego S, Dakshanamurthy S.
PMID: 33619493
bioRxiv. 2021 Mar 22; doi: 10.1101/2021.02.17.431721.

The spread of SARS-CoV-2 and the increasing mortality rates of COVID-19 create an urgent need for treatments, which are currently lacking. Although vaccines have been approved by the FDA for emergency use in the U.S., patients will continue to...

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Policard M, Jain S, Rego S, et al. Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. bioRxiv. 2021;doi: 10.1101/2021.02.17.431721.
Policard, M., Jain, S., Rego, S., & Dakshanamurthy, S. (2021). Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2021.02.17.431721
Policard, Martine, et al. "Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism." bioRxiv : the preprint server for biology vol. (2021). doi: https://doi.org/10.1101/2021.02.17.431721
Policard M, Jain S, Rego S, Dakshanamurthy S. Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. bioRxiv. 2021 Mar 22; doi: 10.1101/2021.02.17.431721. PMID: 33619493; PMCID: PMC7899457.
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Response to Dekker, Stege, and Versteeg.

Journal of the National Cancer Institute

Mandelblatt JS, Zhou X, Small BJ, Ahn J, Zhai W, Ahles T, Extermann M, Graham D, Jacobsen PB, Jim H, McDonald BC, Patel SK, Root JC, Saykin AJ, Cohen HJ, Carroll JE.
PMID: 33823011
J Natl Cancer Inst. 2021 Oct 01;113(10):1436-1437. doi: 10.1093/jnci/djab060.

No abstract available.

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Mandelblatt JS, Zhou X, Small BJ, et al. Response to Dekker, Stege, and Versteeg. J Natl Cancer Inst. 2021;113(10):1436-1437doi: 10.1093/jnci/djab060.
Mandelblatt, J. S., Zhou, X., Small, B. J., Ahn, J., Zhai, W., Ahles, T., Extermann, M., Graham, D., Jacobsen, P. B., Jim, H., McDonald, B. C., Patel, S. K., Root, J. C., Saykin, A. J., Cohen, H. J., & Carroll, J. E. (2021). Response to Dekker, Stege, and Versteeg. Journal of the National Cancer Institute, 113(10), 1436-1437. https://doi.org/10.1093/jnci/djab060
Mandelblatt, Jeanne S, et al. "Response to Dekker, Stege, and Versteeg." Journal of the National Cancer Institute vol. 113,10 (2021): 1436-1437. doi: https://doi.org/10.1093/jnci/djab060
Mandelblatt JS, Zhou X, Small BJ, Ahn J, Zhai W, Ahles T, Extermann M, Graham D, Jacobsen PB, Jim H, McDonald BC, Patel SK, Root JC, Saykin AJ, Cohen HJ, Carroll JE. Response to Dekker, Stege, and Versteeg. J Natl Cancer Inst. 2021 Oct 01;113(10):1436-1437. doi: 10.1093/jnci/djab060. PMID: 33823011; PMCID: PMC8486326.
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Improved irritative voiding symptoms 3 years after stereotactic body radiation therapy for prostate cancer.

Frontiers in oncology

Rana Z, Cyr RA, Chen LN, Kim BS, Moures RA, Yung TM, Lei S, Collins BT, Suy S, Dritschilo A, Lynch JH, Collins SP.
PMID: 25374844
Front Oncol. 2014 Oct 21;4:290. doi: 10.3389/fonc.2014.00290. eCollection 2014.

BACKGROUND: Irritative voiding symptoms are common in elderly men and following prostate radiotherapy. There is limited clinical data on the impact of hypofractionated treatment on irritative voiding symptoms. This study sought to evaluate urgency, frequency, and nocturia following stereotactic...

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Rana Z, Cyr RA, Chen LN, et al. Improved irritative voiding symptoms 3 years after stereotactic body radiation therapy for prostate cancer. Front Oncol. 2014;4:290doi: 10.3389/fonc.2014.00290.
Rana, Z., Cyr, R. A., Chen, L. N., Kim, B. S., Moures, R. A., Yung, T. M., Lei, S., Collins, B. T., Suy, S., Dritschilo, A., Lynch, J. H., & Collins, S. P. (2014). Improved irritative voiding symptoms 3 years after stereotactic body radiation therapy for prostate cancer. Frontiers in oncology, 4290. https://doi.org/10.3389/fonc.2014.00290
Rana, Zaker, et al. "Improved irritative voiding symptoms 3 years after stereotactic body radiation therapy for prostate cancer." Frontiers in oncology vol. 4 (2014): 290. doi: https://doi.org/10.3389/fonc.2014.00290
Rana Z, Cyr RA, Chen LN, Kim BS, Moures RA, Yung TM, Lei S, Collins BT, Suy S, Dritschilo A, Lynch JH, Collins SP. Improved irritative voiding symptoms 3 years after stereotactic body radiation therapy for prostate cancer. Front Oncol. 2014 Oct 21;4:290. doi: 10.3389/fonc.2014.00290. eCollection 2014. PMID: 25374844; PMCID: PMC4204455.
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Expression of a Secreted Fibroblast Growth Factor Binding Protein-1 (FGFBP1) in Angioproliferative Kaposi Sarcoma.

Journal of AIDS & clinical research

Ray PE, Al-Attar A, Liu XH, Das JR, Tassi E, Wellstein A.
PMID: 25429350
J AIDS Clin Res. 2014 Jun;5(6). doi: 10.4172/2155-6113.1000309.

OBJECTIVE: Kaposi's sarcoma (KS) is an angioproliferative disease frequently seen in patients with the acquired immunodeficiency syndrome (AIDS). Previous studies suggest that the HIV-1 protein Tat and Fibroblast Growth Factor 2 (FGF-2) have synergistic angiogenic effects in AIDS-KS tumors....

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Ray PE, Al-Attar A, Liu XH, et al. Expression of a Secreted Fibroblast Growth Factor Binding Protein-1 (FGFBP1) in Angioproliferative Kaposi Sarcoma. J AIDS Clin Res. 2014;5(6)doi: 10.4172/2155-6113.1000309.
Ray, P. E., Al-Attar, A., Liu, X. H., Das, J. R., Tassi, E., & Wellstein, A. (2014). Expression of a Secreted Fibroblast Growth Factor Binding Protein-1 (FGFBP1) in Angioproliferative Kaposi Sarcoma. Journal of AIDS & clinical research, 5(6), . https://doi.org/10.4172/2155-6113.1000309
Ray, Patricio E, et al. "Expression of a Secreted Fibroblast Growth Factor Binding Protein-1 (FGFBP1) in Angioproliferative Kaposi Sarcoma." Journal of AIDS & clinical research vol. 5,6 (2014). doi: https://doi.org/10.4172/2155-6113.1000309
Ray PE, Al-Attar A, Liu XH, Das JR, Tassi E, Wellstein A. Expression of a Secreted Fibroblast Growth Factor Binding Protein-1 (FGFBP1) in Angioproliferative Kaposi Sarcoma. J AIDS Clin Res. 2014 Jun;5(6). doi: 10.4172/2155-6113.1000309. PMID: 25429350; PMCID: PMC4241576.
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Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes.

Nucleic acids research

White SM, Snyder MP, Yi C.
PMID: 34850122
Nucleic Acids Res. 2021 Dec 02;49(21):12196-12210. doi: 10.1093/nar/gkab1105.

The term 'super enhancers' (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis...

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White SM, Snyder MP, Yi C. Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. Nucleic Acids Res. 2021;49(21):12196-12210doi: 10.1093/nar/gkab1105.
White, S. M., Snyder, M. P., & Yi, C. (2021). Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. Nucleic acids research, 49(21), 12196-12210. https://doi.org/10.1093/nar/gkab1105
White, Shannon M, et al. "Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes." Nucleic acids research vol. 49,21 (2021): 12196-12210. doi: https://doi.org/10.1093/nar/gkab1105
White SM, Snyder MP, Yi C. Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. Nucleic Acids Res. 2021 Dec 02;49(21):12196-12210. doi: 10.1093/nar/gkab1105. PMID: 34850122; PMCID: PMC8643643.
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Immune-Related Circulating miR-125b-5p and miR-99a-5p Reveal a High Recurrence Risk Group of Pancreatic Cancer Patients after Tumor Resection.

Applied sciences (Basel, Switzerland)

Vietsch EE, Peran I, Suker M, van den Bosch TPP, van der Sijde F, Kros JM, van Eijck CHJ, Wellstein A.
PMID: 34484811
Appl Sci (Basel). 2019 Nov 02;9(22). doi: 10.3390/app9224784. Epub 2019 Nov 08.

Clinical follow-up aided by changes in the expression of circulating microRNAs (miRs) may improve prognostication of pancreatic ductal adenocarcinoma (PDAC) patients. Changes in 179 circulating miRs due to cancer progression in the transgenic

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Vietsch EE, Peran I, Suker M, et al. Immune-Related Circulating miR-125b-5p and miR-99a-5p Reveal a High Recurrence Risk Group of Pancreatic Cancer Patients after Tumor Resection. Appl Sci (Basel). 2019;9(22)doi: 10.3390/app9224784.
Vietsch, E. E., Peran, I., Suker, M., van den Bosch, T. P. P., van der Sijde, F., Kros, J. M., van Eijck, C. H. J., & Wellstein, A. (2019). Immune-Related Circulating miR-125b-5p and miR-99a-5p Reveal a High Recurrence Risk Group of Pancreatic Cancer Patients after Tumor Resection. Applied sciences (Basel, Switzerland), 9(22), . https://doi.org/10.3390/app9224784
Vietsch, Eveline E, et al. "Immune-Related Circulating miR-125b-5p and miR-99a-5p Reveal a High Recurrence Risk Group of Pancreatic Cancer Patients after Tumor Resection." Applied sciences (Basel, Switzerland) vol. 9,22 (2019). doi: https://doi.org/10.3390/app9224784
Vietsch EE, Peran I, Suker M, van den Bosch TPP, van der Sijde F, Kros JM, van Eijck CHJ, Wellstein A. Immune-Related Circulating miR-125b-5p and miR-99a-5p Reveal a High Recurrence Risk Group of Pancreatic Cancer Patients after Tumor Resection. Appl Sci (Basel). 2019 Nov 02;9(22). doi: 10.3390/app9224784. Epub 2019 Nov 08. PMID: 34484811; PMCID: PMC8415800.
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RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells.

Bio-protocol

Zhang YW, Nasto RE, Jablonski SA, Serebriiskii IG, Surana R, Murray J, Johnson M, Riggins RB, Clarke R, Golemis EA, Weiner LM.
PMID: 29250574
Bio Protoc. 2017;7(15). doi: 10.21769/BioProtoc.2435. Epub 2017 Aug 05.

RNAi screening technology has revealed unknown determinants of various biological signaling pathways in biomedical studies. This protocol provided detailed information about how to use RNAi screening to identify proliferation determinants in breast tumor cells. siRNA-based libraries targeting against Estrogen...

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Zhang YW, Nasto RE, Jablonski SA, et al. RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells. Bio Protoc. 2017;7(15)doi: 10.21769/BioProtoc.2435.
Zhang, Y. W., Nasto, R. E., Jablonski, S. A., Serebriiskii, I. G., Surana, R., Murray, J., Johnson, M., Riggins, R. B., Clarke, R., Golemis, E. A., & Weiner, L. M. (2017). RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells. Bio-protocol, 7(15), . https://doi.org/10.21769/BioProtoc.2435
Zhang, Yong-Wei, et al. "RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells." Bio-protocol vol. 7,15 (2017). doi: https://doi.org/10.21769/BioProtoc.2435
Zhang YW, Nasto RE, Jablonski SA, Serebriiskii IG, Surana R, Murray J, Johnson M, Riggins RB, Clarke R, Golemis EA, Weiner LM. RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells. Bio Protoc. 2017;7(15). doi: 10.21769/BioProtoc.2435. Epub 2017 Aug 05. PMID: 29250574; PMCID: PMC5730085.
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Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method.

Oncotarget

Wathieu H, Issa NT, Fernandez AI, Mohandoss M, Tiek DM, Franke JL, Byers SW, Riggins RB, Dakshanamurthy S.
PMID: 29190967
Oncotarget. 2017 Oct 09;8(54):92926-92942. doi: 10.18632/oncotarget.21669. eCollection 2017 Nov 03.

Triple negative breast cancer (TNBC) is a group of cancers whose heterogeneity and shortage of effective drug therapies has prompted efforts to divide these cancers into molecular subtypes. Our computational platform, entitled GenEx-TNBC, applies concepts in systems biology and...

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Wathieu H, Issa NT, Fernandez AI, et al. Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. Oncotarget. 2017;8(54):92926-92942doi: 10.18632/oncotarget.21669.
Wathieu, H., Issa, N. T., Fernandez, A. I., Mohandoss, M., Tiek, D. M., Franke, J. L., Byers, S. W., Riggins, R. B., & Dakshanamurthy, S. (2017). Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. Oncotarget, 8(54), 92926-92942. https://doi.org/10.18632/oncotarget.21669
Wathieu, Henri, et al. "Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method." Oncotarget vol. 8,54 (2017): 92926-92942. doi: https://doi.org/10.18632/oncotarget.21669
Wathieu H, Issa NT, Fernandez AI, Mohandoss M, Tiek DM, Franke JL, Byers SW, Riggins RB, Dakshanamurthy S. Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. Oncotarget. 2017 Oct 09;8(54):92926-92942. doi: 10.18632/oncotarget.21669. eCollection 2017 Nov 03. PMID: 29190967; PMCID: PMC5696233.
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Cancer health disparities in racial/ethnic minorities in the United States.

British journal of cancer

Zavala VA, Bracci PM, Carethers JM, Carvajal-Carmona L, Coggins NB, Cruz-Correa MR, Davis M, de Smith AJ, Dutil J, Figueiredo JC, Fox R, Graves KD, Gomez SL, Llera A, Neuhausen SL, Newman L, Nguyen T, Palmer JR, Palmer NR, Pérez-Stable EJ, Piawah S, Rodriquez EJ, Sanabria-Salas MC, Schmit SL, Serrano-Gomez SJ, Stern MC, Weitzel J, Yang JJ, Zabaleta J, Ziv E, Fejerman L.
PMID: 32901135
Br J Cancer. 2021 Jan;124(2):315-332. doi: 10.1038/s41416-020-01038-6. Epub 2020 Sep 09.

There are well-established disparities in cancer incidence and outcomes by race/ethnicity that result from the interplay between structural, socioeconomic, socio-environmental, behavioural and biological factors. However, large research studies designed to investigate factors contributing to cancer aetiology and progression have...

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Zavala VA, Bracci PM, Carethers JM, et al. Cancer health disparities in racial/ethnic minorities in the United States. Br J Cancer. 2020;124(2):315-332doi: 10.1038/s41416-020-01038-6.
Zavala, V. A., Bracci, P. M., Carethers, J. M., Carvajal-Carmona, L., Coggins, N. B., Cruz-Correa, M. R., Davis, M., de Smith, A. J., Dutil, J., Figueiredo, J. C., Fox, R., Graves, K. D., Gomez, S. L., Llera, A., Neuhausen, S. L., Newman, L., Nguyen, T., Palmer, J. R., Palmer, N. R., Pérez-Stable, E. J., Piawah, S., Rodriquez, E. J., Sanabria-Salas, M. C., Schmit, S. L., Serrano-Gomez, S. J., Stern, M. C., Weitzel, J., Yang, J. J., Zabaleta, J., Ziv, E., & Fejerman, L. (2021). Cancer health disparities in racial/ethnic minorities in the United States. British journal of cancer, 124(2), 315-332. https://doi.org/10.1038/s41416-020-01038-6
Zavala, Valentina A, et al. "Cancer health disparities in racial/ethnic minorities in the United States." British journal of cancer vol. 124,2 (2021): 315-332. doi: https://doi.org/10.1038/s41416-020-01038-6
Zavala VA, Bracci PM, Carethers JM, Carvajal-Carmona L, Coggins NB, Cruz-Correa MR, Davis M, de Smith AJ, Dutil J, Figueiredo JC, Fox R, Graves KD, Gomez SL, Llera A, Neuhausen SL, Newman L, Nguyen T, Palmer JR, Palmer NR, Pérez-Stable EJ, Piawah S, Rodriquez EJ, Sanabria-Salas MC, Schmit SL, Serrano-Gomez SJ, Stern MC, Weitzel J, Yang JJ, Zabaleta J, Ziv E, Fejerman L. Cancer health disparities in racial/ethnic minorities in the United States. Br J Cancer. 2021 Jan;124(2):315-332. doi: 10.1038/s41416-020-01038-6. Epub 2020 Sep 09. PMID: 32901135; PMCID: PMC7852513.
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Screening for psychosocial distress among patients with cancer: implications for clinical practice, healthcare policy, and dissemination to enhance cancer survivorship.

Translational behavioral medicine

Ehlers SL, Davis K, Bluethmann SM, Quintiliani LM, Kendall J, Ratwani RM, Diefenbach MA, Graves KD.
PMID: 30566662
Transl Behav Med. 2019 Mar 01;9(2):282-291. doi: 10.1093/tbm/iby123.

Accreditation standards are at the forefront of evolving healthcare systems, setting metrics for high-quality care. Healthcare outcomes (health, experience, cost, provider satisfaction/burn out) are becoming mutual goals of the patient, provider, payer, and healthcare system. Achieving high-quality outcomes in...

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Ehlers SL, Davis K, Bluethmann SM, et al. Screening for psychosocial distress among patients with cancer: implications for clinical practice, healthcare policy, and dissemination to enhance cancer survivorship. Transl Behav Med. 2019;9(2):282-291doi: 10.1093/tbm/iby123.
Ehlers, S. L., Davis, K., Bluethmann, S. M., Quintiliani, L. M., Kendall, J., Ratwani, R. M., Diefenbach, M. A., & Graves, K. D. (2019). Screening for psychosocial distress among patients with cancer: implications for clinical practice, healthcare policy, and dissemination to enhance cancer survivorship. Translational behavioral medicine, 9(2), 282-291. https://doi.org/10.1093/tbm/iby123
Ehlers, Shawna L, et al. "Screening for psychosocial distress among patients with cancer: implications for clinical practice, healthcare policy, and dissemination to enhance cancer survivorship." Translational behavioral medicine vol. 9,2 (2019): 282-291. doi: https://doi.org/10.1093/tbm/iby123
Ehlers SL, Davis K, Bluethmann SM, Quintiliani LM, Kendall J, Ratwani RM, Diefenbach MA, Graves KD. Screening for psychosocial distress among patients with cancer: implications for clinical practice, healthcare policy, and dissemination to enhance cancer survivorship. Transl Behav Med. 2019 Mar 01;9(2):282-291. doi: 10.1093/tbm/iby123. PMID: 30566662; PMCID: PMC6610173.
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Central Cholinergic Synapse Formation in Optimized Primary Septal-Hippocampal Co-cultures.

Cellular and molecular neurobiology

Djemil S, Ressel CR, Abdel-Ghani M, Schneeweis AK, Pak DTS.
PMID: 32860154
Cell Mol Neurobiol. 2021 Nov;41(8):1787-1799. doi: 10.1007/s10571-020-00948-6. Epub 2020 Aug 28.

Septal innervation of basal forebrain cholinergic neurons to the hippocampus is critical for normal learning and memory and is severely degenerated in Alzheimer's disease. To understand the molecular events underlying physiological cholinergic synaptogenesis and remodeling, as well as pathological...

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Djemil S, Ressel CR, Abdel-Ghani M, et al. Central Cholinergic Synapse Formation in Optimized Primary Septal-Hippocampal Co-cultures. Cell Mol Neurobiol. 2020;41(8):1787-1799doi: 10.1007/s10571-020-00948-6.
Djemil, S., Ressel, C. R., Abdel-Ghani, M., Schneeweis, A. K., & Pak, D. T. S. (2021). Central Cholinergic Synapse Formation in Optimized Primary Septal-Hippocampal Co-cultures. Cellular and molecular neurobiology, 41(8), 1787-1799. https://doi.org/10.1007/s10571-020-00948-6
Djemil, Sarra, et al. "Central Cholinergic Synapse Formation in Optimized Primary Septal-Hippocampal Co-cultures." Cellular and molecular neurobiology vol. 41,8 (2021): 1787-1799. doi: https://doi.org/10.1007/s10571-020-00948-6
Djemil S, Ressel CR, Abdel-Ghani M, Schneeweis AK, Pak DTS. Central Cholinergic Synapse Formation in Optimized Primary Septal-Hippocampal Co-cultures. Cell Mol Neurobiol. 2021 Nov;41(8):1787-1799. doi: 10.1007/s10571-020-00948-6. Epub 2020 Aug 28. PMID: 32860154; PMCID: PMC7914286.
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Machine and deep learning approaches for cancer drug repurposing.

Seminars in cancer biology

Issa NT, Stathias V, Schürer S, Dakshanamurthy S.
PMID: 31904426
Semin Cancer Biol. 2021 Jan;68:132-142. doi: 10.1016/j.semcancer.2019.12.011. Epub 2020 Jan 03.

Knowledge of the underpinnings of cancer initiation, progression and metastasis has increased exponentially in recent years. Advanced "omics" coupled with machine learning and artificial intelligence (deep learning) methods have helped elucidate targets and pathways critical to those processes that...

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Issa NT, Stathias V, Schürer S, et al. Machine and deep learning approaches for cancer drug repurposing. Semin Cancer Biol. 2020;68:132-142doi: 10.1016/j.semcancer.2019.12.011.
Issa, N. T., Stathias, V., Schürer, S., & Dakshanamurthy, S. (2021). Machine and deep learning approaches for cancer drug repurposing. Seminars in cancer biology, 68132-142. https://doi.org/10.1016/j.semcancer.2019.12.011
Issa, Naiem T, et al. "Machine and deep learning approaches for cancer drug repurposing." Seminars in cancer biology vol. 68 (2021): 132-142. doi: https://doi.org/10.1016/j.semcancer.2019.12.011
Issa NT, Stathias V, Schürer S, Dakshanamurthy S. Machine and deep learning approaches for cancer drug repurposing. Semin Cancer Biol. 2021 Jan;68:132-142. doi: 10.1016/j.semcancer.2019.12.011. Epub 2020 Jan 03. PMID: 31904426; PMCID: PMC7723306.
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