The Human Pathology Atlas for deciphering the prognostic features of human cancers

TY - JOUR

T1 - The Human Pathology Atlas for deciphering the prognostic features of human cancers

AU - Yuan, Meng

AU - Zhang, Cheng

AU - Von Feilitzen, Kalle

AU - Zwahlen, Martin

AU - Shi, Mengnan

AU - Li, Xiangyu

AU - Yang, Hong

AU - Song, Xiya

AU - Turkez, Hasan

AU - Uhlén, Mathias

AU - Mardinoglu, Adil

N1 - Publisher Copyright: © 2024 The Author(s)

PY - 2025/1

Y1 - 2025/1

N2 - Background: Cancer is one of the leading causes of mortality worldwide, highlighting the urgent need for a deeper molecular understanding and the development of personalized treatments. The present study aims to establish a solid association between gene expression and patient survival outcomes to enhance the utility of the Human Pathology Atlas for cancer research. Methods: In this updated analysis, we examined the expression profiles of 6918 patients across 21 cancer types. We integrated data from 10 independent cancer cohorts, creating a cross-validated, reliable collection of prognostic genes. We applied systems biology approach to identify the association between gene expression profiles and patient survival outcomes. We further constructed prognostic regulatory networks for kidney renal clear cell carcinoma (KIRC) and liver hepatocellular carcinoma (LIHC), which elucidate the molecular underpinnings associated with patient survival in these cancers. Findings: We observed that gene expression during the transition from normal to tumorous tissue exhibited diverse shifting patterns in their original tissue locations. Significant correlations between gene expression and patient survival outcomes were identified in KIRC and LIHC among the major cancer types. Additionally, the prognostic regulatory network established for these two cancers showed the indicative capabilities of the Human Pathology Atlas and provides actionable insights for cancer research. Interpretation: The updated Human Pathology Atlas provides a significant foundation for precision oncology and the formulation of personalized treatment strategies. These findings deepen our understanding of cancer biology and have the potential to advance targeted therapeutic approaches in clinical practice. Funding: The Knut and Alice Wallenberg Foundation ( 72110), the China Scholarship Council (Grant No. 202006940003).

AB - Background: Cancer is one of the leading causes of mortality worldwide, highlighting the urgent need for a deeper molecular understanding and the development of personalized treatments. The present study aims to establish a solid association between gene expression and patient survival outcomes to enhance the utility of the Human Pathology Atlas for cancer research. Methods: In this updated analysis, we examined the expression profiles of 6918 patients across 21 cancer types. We integrated data from 10 independent cancer cohorts, creating a cross-validated, reliable collection of prognostic genes. We applied systems biology approach to identify the association between gene expression profiles and patient survival outcomes. We further constructed prognostic regulatory networks for kidney renal clear cell carcinoma (KIRC) and liver hepatocellular carcinoma (LIHC), which elucidate the molecular underpinnings associated with patient survival in these cancers. Findings: We observed that gene expression during the transition from normal to tumorous tissue exhibited diverse shifting patterns in their original tissue locations. Significant correlations between gene expression and patient survival outcomes were identified in KIRC and LIHC among the major cancer types. Additionally, the prognostic regulatory network established for these two cancers showed the indicative capabilities of the Human Pathology Atlas and provides actionable insights for cancer research. Interpretation: The updated Human Pathology Atlas provides a significant foundation for precision oncology and the formulation of personalized treatment strategies. These findings deepen our understanding of cancer biology and have the potential to advance targeted therapeutic approaches in clinical practice. Funding: The Knut and Alice Wallenberg Foundation ( 72110), the China Scholarship Council (Grant No. 202006940003).

KW - Cancer

KW - Survival

KW - Systems biology

KW - Transcriptomics

UR - http://www.scopus.com/inward/record.url?scp=85211197830&partnerID=8YFLogxK

U2 - 10.1016/j.ebiom.2024.105495

DO - 10.1016/j.ebiom.2024.105495

M3 - Article

C2 - 39662180

AN - SCOPUS:85211197830

SN - 2352-3964

VL - 111

JO - EBioMedicine

JF - EBioMedicine

M1 - 105495

ER -