Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting
<h3>Background</h3><p dir="ltr">Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical p...
محفوظ في:
| المؤلف الرئيسي: | |
|---|---|
| مؤلفون آخرون: | , , , , , , , , , , , , , |
| منشور في: |
2022
|
| الموضوعات: | |
| الوسوم: |
إضافة وسم
لا توجد وسوم, كن أول من يضع وسما على هذه التسجيلة!
|
| _version_ | 1864513516840419328 |
|---|---|
| author | Shimaa Sherif (12862990) |
| author2 | Raghvendra Mall (581171) Hossam Almeer (9771875) Adviti Naik (673163) Abdulaziz Al Homaid (13890984) Remy Thomas (702843) Jessica Roelands (7516439) Sathiya Narayanan (13890987) Mahmoud Gasim Mohamed (13890990) Shahinaz Bedri (4480651) Salha Bujassoum Al-Bader (4264198) Kulsoom Junejo (9327448) Davide Bedognetti (2632474) Wouter Hendrickx (44559) Julie Decock (44558) |
| author2_role | author author author author author author author author author author author author author author |
| author_facet | Shimaa Sherif (12862990) Raghvendra Mall (581171) Hossam Almeer (9771875) Adviti Naik (673163) Abdulaziz Al Homaid (13890984) Remy Thomas (702843) Jessica Roelands (7516439) Sathiya Narayanan (13890987) Mahmoud Gasim Mohamed (13890990) Shahinaz Bedri (4480651) Salha Bujassoum Al-Bader (4264198) Kulsoom Junejo (9327448) Davide Bedognetti (2632474) Wouter Hendrickx (44559) Julie Decock (44558) |
| author_role | author |
| dc.creator.none.fl_str_mv | Shimaa Sherif (12862990) Raghvendra Mall (581171) Hossam Almeer (9771875) Adviti Naik (673163) Abdulaziz Al Homaid (13890984) Remy Thomas (702843) Jessica Roelands (7516439) Sathiya Narayanan (13890987) Mahmoud Gasim Mohamed (13890990) Shahinaz Bedri (4480651) Salha Bujassoum Al-Bader (4264198) Kulsoom Junejo (9327448) Davide Bedognetti (2632474) Wouter Hendrickx (44559) Julie Decock (44558) |
| dc.date.none.fl_str_mv | 2022-09-30T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1186/s12967-022-03654-7 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Immune-related_3-lncRNA_signature_with_prognostic_connotation_in_a_multi-cancer_setting/25609443 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Biochemistry and cell biology Biomedical and clinical sciences Oncology and carcinogenesis lncRNA ICR Immune checkpoint Prognostic Immune favorable |
| dc.title.none.fl_str_mv | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <h3>Background</h3><p dir="ltr">Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly expanding.</p><h3>Methods</h3><p dir="ltr">We developed a multi-step process to identify immune-related long non-coding RNA signatures with prognostic connotation in multiple TCGA solid cancer datasets.</p><h3>Results</h3><p dir="ltr">Using the breast cancer dataset as a discovery cohort we found 2988 differentially expressed lncRNAs between immune favorable and unfavorable tumors, as defined by the immunologic constant of rejection (ICR) gene signature. Mapping of the lncRNAs to a coding-non-coding network identified 127 proxy protein-coding genes that are enriched in immune-related diseases and functions. Next, we defined two distinct 20-lncRNA prognostic signatures that show a stronger effect on overall survival than the ICR signature in multiple solid cancers. Furthermore, we found a 3 lncRNA signature that demonstrated prognostic significance across 5 solid cancer types with a stronger association with clinical outcome than ICR. Moreover, this 3 lncRNA signature showed additional prognostic significance in uterine corpus endometrial carcinoma and cervical squamous cell carcinoma and endocervical adenocarcinoma as compared to ICR.</p><h3>Conclusion</h3><p dir="ltr">We identified an immune-related 3-lncRNA signature with prognostic connotation in multiple solid cancer types which performed equally well and in some cases better than the 20-gene ICR signature, indicating that it could be used as a minimal informative signature for clinical implementation.</p><h2>Other Information</h2><p dir="ltr">Published in: Journal of Translational Medicine<br>License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s12967-022-03654-7" target="_blank">https://dx.doi.org/10.1186/s12967-022-03654-7</a></p><p><br></p><p dir="ltr">Additional institutions affiliated with: Hamad Medical Corporation, Hamad General Hospital - HMC</p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_dd398285334cbe2e9bcc32f6f6b73ae9 |
| identifier_str_mv | 10.1186/s12967-022-03654-7 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/25609443 |
| publishDate | 2022 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer settingShimaa Sherif (12862990)Raghvendra Mall (581171)Hossam Almeer (9771875)Adviti Naik (673163)Abdulaziz Al Homaid (13890984)Remy Thomas (702843)Jessica Roelands (7516439)Sathiya Narayanan (13890987)Mahmoud Gasim Mohamed (13890990)Shahinaz Bedri (4480651)Salha Bujassoum Al-Bader (4264198)Kulsoom Junejo (9327448)Davide Bedognetti (2632474)Wouter Hendrickx (44559)Julie Decock (44558)Biological sciencesBiochemistry and cell biologyBiomedical and clinical sciencesOncology and carcinogenesislncRNAICRImmune checkpointPrognosticImmune favorable<h3>Background</h3><p dir="ltr">Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly expanding.</p><h3>Methods</h3><p dir="ltr">We developed a multi-step process to identify immune-related long non-coding RNA signatures with prognostic connotation in multiple TCGA solid cancer datasets.</p><h3>Results</h3><p dir="ltr">Using the breast cancer dataset as a discovery cohort we found 2988 differentially expressed lncRNAs between immune favorable and unfavorable tumors, as defined by the immunologic constant of rejection (ICR) gene signature. Mapping of the lncRNAs to a coding-non-coding network identified 127 proxy protein-coding genes that are enriched in immune-related diseases and functions. Next, we defined two distinct 20-lncRNA prognostic signatures that show a stronger effect on overall survival than the ICR signature in multiple solid cancers. Furthermore, we found a 3 lncRNA signature that demonstrated prognostic significance across 5 solid cancer types with a stronger association with clinical outcome than ICR. Moreover, this 3 lncRNA signature showed additional prognostic significance in uterine corpus endometrial carcinoma and cervical squamous cell carcinoma and endocervical adenocarcinoma as compared to ICR.</p><h3>Conclusion</h3><p dir="ltr">We identified an immune-related 3-lncRNA signature with prognostic connotation in multiple solid cancer types which performed equally well and in some cases better than the 20-gene ICR signature, indicating that it could be used as a minimal informative signature for clinical implementation.</p><h2>Other Information</h2><p dir="ltr">Published in: Journal of Translational Medicine<br>License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s12967-022-03654-7" target="_blank">https://dx.doi.org/10.1186/s12967-022-03654-7</a></p><p><br></p><p dir="ltr">Additional institutions affiliated with: Hamad Medical Corporation, Hamad General Hospital - HMC</p>2022-09-30T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1186/s12967-022-03654-7https://figshare.com/articles/journal_contribution/Immune-related_3-lncRNA_signature_with_prognostic_connotation_in_a_multi-cancer_setting/25609443CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/256094432022-09-30T03:00:00Z |
| spellingShingle | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting Shimaa Sherif (12862990) Biological sciences Biochemistry and cell biology Biomedical and clinical sciences Oncology and carcinogenesis lncRNA ICR Immune checkpoint Prognostic Immune favorable |
| status_str | publishedVersion |
| title | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| title_full | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| title_fullStr | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| title_full_unstemmed | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| title_short | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| title_sort | Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting |
| topic | Biological sciences Biochemistry and cell biology Biomedical and clinical sciences Oncology and carcinogenesis lncRNA ICR Immune checkpoint Prognostic Immune favorable |