Search

Your search keyword '"Sherif, Shimaa"' showing total 32 results
Start Over Author "Sherif, Shimaa"
32 results on '"Sherif, Shimaa"'

1. A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer

Author

Mason, Mike, Lapuente-Santana, Óscar, Halkola, Anni S., Wang, Wenyu, Mall, Raghvendra, Xiao, Xu, Kaufman, Jacob, Fu, Jingxin, Pfeil, Jacob, Banerjee, Jineta, Chung, Verena, Chang, Han, Chasalow, Scott D., Lin, Hung Ying, Chai, Rongrong, Yu, Thomas, Finotello, Francesca, Mirtti, Tuomas, Mäyränpää, Mikko I., Bao, Jie, Verschuren, Emmy W., Ahmed, Eiman I., Ceccarelli, Michele, Miller, Lance D., Monaco, Gianni, Hendrickx, Wouter R. L., Sherif, Shimaa, Yang, Lin, Tang, Ming, Gu, Shengqing Stan, Zhang, Wubing, Zhang, Yi, Zeng, Zexian, Das Sahu, Avinash, Liu, Yang, Yang, Wenxian, Bedognetti, Davide, Tang, Jing, Eduati, Federica, Laajala, Teemu D., Geese, William J., Guinney, Justin, Szustakowski, Joseph D., Vincent, Benjamin G., and Carbone, David P.

Published
2024
Full Text
View/download PDF

2. An integrated tumor, immune and microbiome atlas of colon cancer.

Author

Roelands, Jessica, Kuppen, Peter, Ahmed, Eiman, Mall, Raghvendra, Masoodi, Tariq, Singh, Parul, Monaco, Gianni, Raynaud, Christophe, de Miranda, Noel, Ferraro, Luigi, Carneiro-Lobo, Tatiana, Syed, Najeeb, Rawat, Arun, Awad, Amany, Decock, Julie, Mifsud, William, Miller, Lance, Sherif, Shimaa, Mohamed, Mahmoud, Rinchai, Darawan, Van den Eynde, Marc, Sayaman, Rosalyn, Ziv, Elad, Bertucci, Francois, Petkar, Mahir, Lorenz, Stephan, Mathew, Lisa, Wang, Kun, Murugesan, Selvasankar, Chaussabel, Damien, Vahrmeijer, Alexander, Wang, Ena, Ceccarelli, Anna, Fakhro, Khalid, Zoppoli, Gabriele, Ballestrero, Alberto, Tollenaar, Rob, Marincola, Francesco, Galon, Jérôme, Khodor, Souhaila, Ceccarelli, Michele, Hendrickx, Wouter, and Bedognetti, Davide

Subjects
Humans, Cohort Studies, Biomarkers, Tumor, Colonic Neoplasms, Transcriptome, Tumor Microenvironment
Abstract

The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.

Published
2023

7. The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Published
2022
Full Text
View/download PDF

9. A population study of clinically actionable genetic variation affecting drug response from the Middle East

Author

Jithesh, Puthen Veettil, Abuhaliqa, Mohammed, Syed, Najeeb, Ahmed, Ikhlak, El Anbari, Mohammed, Bastaki, Kholoud, Sherif, Shimaa, Umlai, Umm-Kulthum, Jan, Zainab, Gandhi, Geethanjali, Manickam, Chidambaram, Selvaraj, Senthil, George, Chinnu, Bangarusamy, Dhinoth, Abdel-latif, Rania, Al-Shafai, Mashael, Tatari-Calderone, Zohreh, Estivill, Xavier, and Pirmohamed, Munir

Published
2022
Full Text
View/download PDF

12. A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer

Author

Mason, Mike, primary, Lapuente-Santana, Óscar, additional, Halkola, Anni S., additional, Wang, Wenyu, additional, Mall, Raghvendra, additional, Xiao, Xu, additional, Kaufman, Jacob, additional, Fu, Jingxin, additional, Pfeil, Jacob, additional, Banerjee, Jineta, additional, Chung, Verena, additional, Chang, Han, additional, Chasalow, Scott D., additional, Lin, Hung Ying, additional, Chai, Rongrong, additional, Yu, Thomas, additional, Finotello, Francesca, additional, Mirtti, Tuomas, additional, Mäyränpää, Mikko I., additional, Bao, Jie, additional, Verschuren, Emmy W., additional, Ahmed, Eiman I., additional, Ceccarelli, Michele, additional, Miller, Lance D., additional, Monaco, Gianni, additional, Hendrickx, Wouter R.L., additional, Sherif, Shimaa, additional, Yang, Lin, additional, Tang, Ming, additional, Gu, Shengqing Stan, additional, Zhang, Wubing, additional, Zhang, Yi, additional, Zeng, Zexian, additional, Sahu, Avinash Das, additional, Liu, Yang, additional, Yang, Wenxian, additional, Bedognetti, Davide, additional, Tang, Jing, additional, Eduati, Federica, additional, Laajala, Teemu D., additional, Geese, William J., additional, Guinney, Justin, additional, Szustakowski, Joseph D., additional, Carbone, David P., additional, and Vincent, Benjamin G., additional

Published
2022
Full Text
View/download PDF

15. Additional file 9 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Author

Sherif, Shimaa, Mall, Raghvendra, Almeer, Hossam, Naik, Adviti, Al Homaid, Abdulaziz, Thomas, Remy, Roelands, Jessica, Narayanan, Sathiya, Mohamed, Mahmoud Gasim, Bedri, Shahinaz, Al-Bader, Salha Bujassoum, Junejo, Kulsoom, Bedognetti, Davide, Hendrickx, Wouter, and Decock, Julie

Abstract

Additional file 9: Correlation of 3 ir-lncRNA signature with immune subpopulations across tumor types. Pearson correlation heatmap between immune cell subpopulation enrichment scores and 3 ir-lncRNA scores.

Published
2022
Full Text
View/download PDF

16. Additional file 4 of The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Subjects
bacteria, biochemical phenomena, metabolism, and nutrition
Abstract

Additional file 4: Supplementary Fig. 4. Overall survival across Immune subtypes. (A) Kaplan-Meier overall survival curve for immune subtypes within Wilms tumor. (B) Kaplan-Meier overall survival curve for immune subtypes within Rhabdoid tumor. (C) Kaplan-Meier overall survival curve for immune subtypes within high risk NBL with MYCN amplification tumors. (D) Forest plot showing HRs (overall survival) of immune subtypes within high risk NBL with MYCN amplification tumors; S1, S2, S3, S5 versus S6 (E) Kaplan-Meier overall survival curve for immune subtypes within Intermediate and low risk NBL tumors.

Published
2022
Full Text
View/download PDF

17. Additional file 6 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Author

Sherif, Shimaa, Mall, Raghvendra, Almeer, Hossam, Naik, Adviti, Al Homaid, Abdulaziz, Thomas, Remy, Roelands, Jessica, Narayanan, Sathiya, Mohamed, Mahmoud Gasim, Bedri, Shahinaz, Al-Bader, Salha Bujassoum, Junejo, Kulsoom, Bedognetti, Davide, Hendrickx, Wouter, and Decock, Julie

Abstract

Additional file 6: Prognostic value of ICR classifier across solid cancers. Forest plot showing HRs for death (overall survival) and corresponding 95%-confidence interval for the continuous ICR score and number of patients for each TCGA cancer cohort and RAQA breast cancer cohort. Significant positive HRs are visualized in blue and significant negative HRs are visualized in red. ICR enabled (HR < 1, p-value < 0.05) cancer types are indicated with orange asterisks and ICR disabled (HR > 1, p-value < 0.05) cancers are indicated with purple asterisks.

Published
2022
Full Text
View/download PDF

18. Additional file 3 of The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Subjects
neoplasms
Abstract

Additional file 3: Supplementary Fig. 3. Intrinsic oncogenic pathways and immune infiltration. (A) Heatmap of Pearson correlation between enrichment score (ES) of oncogenic pathways and ICR in pan-cancer, Osteosarcoma and high risk NBL without MYCN amplification. (B) Forest plot of HR of oncogenic pathways enrichment in Osteosarcoma (C) Forest plot of HR of oncogenic pathways enrichment in high risk NBL without MYCN amplification.

Published
2022
Full Text
View/download PDF

19. Additional file 6 of The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Subjects
animal diseases, bacteria, chemical and pharmacologic phenomena, biochemical phenomena, metabolism, and nutrition
Abstract

Additional file 6: Supplementary Fig. 6. CIBERSORTx immune cells proportions (Aggregate) across Immune subtypes. (A) Barplot of the median of proportions of aggregate CIBERSORTx immune cells in the 6 immune subtypes.

Published
2022
Full Text
View/download PDF

20. Additional file 2 of The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Subjects
animal diseases, virus diseases
Abstract

Additional file 2: Supplementary Fig. 2. The Immunologic constant of rejection. (A) Pan-cancer heatmap of ICR gene expression annotated by cancer types, and per-cancer clustering ICR High, medium and low. (B) Boxplot showing the distribution of ICR scores in high risk NBL with MYCN amplification, high risk NBL without MYCN amplification, and Intermediate and low risk NBL (the p value was calculated by two-tailed t-test). (C) Kaplan-Meier of overall survival for ICR High versus ICR low in Wilms tumor. (D) Kaplan-Meier event free survival curve for ICR High + medium (orange) versus ICR low (blue) in Osteosarcoma. (E) Kaplan-Meier of overall survival for ICR High versus ICR low in Rhabdoid tumor.

Published
2022
Full Text
View/download PDF

21. Additional file 5 of The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Subjects
animal diseases, bacteria, chemical and pharmacologic phenomena, biochemical phenomena, metabolism, and nutrition
Abstract

Additional file 5: Supplementary Fig. 5. CIBERSORTx immune cells proportions across Immune subtypes. (A) Barplot of the median of proportions of CIBERSORTx immune cells in the 6 immune subtypes. (B) Boxplots of means of CIBERSORTx immune cells across the immune subtypes.

Published
2022
Full Text
View/download PDF

22. Additional file 8 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Author

Sherif, Shimaa, Mall, Raghvendra, Almeer, Hossam, Naik, Adviti, Al Homaid, Abdulaziz, Thomas, Remy, Roelands, Jessica, Narayanan, Sathiya, Mohamed, Mahmoud Gasim, Bedri, Shahinaz, Al-Bader, Salha Bujassoum, Junejo, Kulsoom, Bedognetti, Davide, Hendrickx, Wouter, and Decock, Julie

Abstract

Additional file 8: Survival curves of 3 ir-lncRNA signature. Overall survival Kaplan-Meier curves in which the 3 ir-lncRNAs signature did not show any significant prognostic value. Dichotomization cutoff of ‘high’ (red) and ‘low’ (cyan) subgroups was based on the optimal cut-off point as determined by a 5-fold cross-validation analysis. Censor points are indicated by vertical lines. P-values were determined by logrank test.

Published
2022
Full Text
View/download PDF

23. Additional file 7 of The immune landscape of solid pediatric tumors

Author

Sherif, Shimaa, Roelands, Jessica, Mifsud, William, Ahmed, Eiman I., Raynaud, Christophe M., Rinchai, Darawan, Sathappan, Abbirami, Maaz, Ata, Saleh, Ayman, Ozer, Erdener, Fakhro, Khalid A., Mifsud, Borbala, Thorsson, Vésteinn, Bedognetti, Davide, and Hendrickx, Wouter R. L.

Subjects
animal diseases, bacteria, chemical and pharmacologic phenomena, biochemical phenomena, metabolism, and nutrition
Abstract

Additional file 7: Supplementary Fig. 7. Heatmap of enrichment scores of immune cells signatures. Left: Across the tumor types. Right: Across the immune subtypes.

Published
2022
Full Text
View/download PDF

24. Additional file 1 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Author

Sherif, Shimaa, Mall, Raghvendra, Almeer, Hossam, Naik, Adviti, Al Homaid, Abdulaziz, Thomas, Remy, Roelands, Jessica, Narayanan, Sathiya, Mohamed, Mahmoud Gasim, Bedri, Shahinaz, Al-Bader, Salha Bujassoum, Junejo, Kulsoom, Bedognetti, Davide, Hendrickx, Wouter, and Decock, Julie

Abstract

Additional file 1: Mapping of differentially expressed ir-lncRNAs to protein coding genes. (A) Diagram representation of the random walk with restart global propagation network algorithm. (B) Walkscore distribution of protein-coding genes in TCGA-BRCA, with cutoff set at walkscore ≥ 0.01 to generate a ranked list of protein-coding genes in proximity of differentially expressed ir-lncRNAs.

Published
2022
Full Text
View/download PDF

27. 520 The immune landscape of pediatric tumors

Author

Sherif, Shimaa, primary, Roelands, Jessica, additional, Mifsud, William, additional, Dason, Blessing, additional, Rinchai, Darawan, additional, Charles, Adrian, additional, Saleh, Ayman, additional, Cugno, Chiara, additional, Fakhro, Khalid, additional, Mifsud, Borbala, additional, Bedognetti, Davide, additional, and Hendrickx, Wouter, additional

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results