Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment

3122 Cancers

This work was supported by U.S. National Institutes of Health (NIH) grants (P01 CA87969; UM1 CA186107; P01 CA55075; UM1 CA167552; U01 CA167552; P50 CA127003 to C.S.F.; R35 CA197735 to S.O.; R01 CA248857 to S.O.; R37 CA225655 to J.K.L.; R50 CA274122 to T.U.); by Cancer Research UK Grand Challenge Award (UK C10674/A27140 to S.O.); by the Stand Up to Cancer Colorectal Cancer Dream Team Translational Research Grant (SU2C-AACR-DT22-17 to C.S.F.), administered by the American Association for Cancer Research, a scientific partner of SU2C; by the BII and SIgN (A*STAR) core fund to M.C.L.; by National Medical Research Council the Open Fund– Young Individual Research Grant (OFYIRG23jan-0049 to M.C.L.); by grant from the Project P Fund to C.S.F.; by grant from The Friends of the Dana-Farber Cancer Institute to S.O.; by grant from the Bennett Family Fund (C.S.F.); and by grant from the Entertainment Industry Foundation through National Colorectal Cancer Research Alliance and SU2C (to C.S.F.). Those grants without non-author PI names supported the NHS and HPFS cohorts. These are cohort infrastructure grants that played important roles in this study. K.H. was supported by fellowship grants from the Uehara Memorial Foundation and the Mitsukoshi Health and Welfare Foundation. J.B. was supported by a grant from the Australia Awards-Endeavour Scholarships and Fellowships Program. K.A. was supported by a grant from Overseas Research Fellowship (JP2018-60083) from Japan Society for the Promotion of Science; J.A.M. received institutional research funding from Boston Biomedical. S.O. is an American Cancer Society Clinical Research Professor (CRP-24-1185864-01-PROF). T.U. was supported by the Prevent Cancer Foundation grant, Harvey V. Fineberg Cancer Prevention Fellowship from Harvard T.H. Chan School of Public Health, Brigham and Women’s Hospital Faculty Career Development Award, an Investigator Initiated Grant from the American Institute for Cancer Research (AICR).

All the code used to produce the results of this study is available at https://github.com/SIgN-CI/TIPC. The TIPC algorithm’s web application can be accessed at https://mspc.bii.a-star.edu.sg/minhn/tipc.html. Further information including the procedures to obtain and access data from the Nurses’ Health Studies and Health Professionals Follow-up Study is described at https://www.nurseshealthstudy.org/researchers (contact email: nhsaccess@channing.harvard.edu) and https://sites.sph.harvard.edu/hpfs/for-collaborators/. Because of participant confidentiality and privacy concerns, data cannot be shared publicly and requests to access NHS/NHSII/HPFS data must be submitted in writing. According to standard controlled access procedures, applications to use NHS/NHSII/HPFS resources will be reviewed by our External Collaborations Committee to verify that the proposed use maintains the protection of the privacy of participants and the confidentiality of the data. Investigators wishing to use NHS/NHSII/HPFS data are asked to submit a brief description of the proposed project (go to https://www.nurseshealthstudy.org/researchers (contact email: nhsaccess@channing.harvard.edu) and https://sites.sph.harvard.edu/hpfs/for-collaborators/ for details.