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| Status |
Public on Sep 13, 2024 |
| Title |
Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Tertiary lymphoid structures (TLS) are associated with improved response in solid tumors treated with immune checkpoint blockade (ICB), but understanding of their clinical significance and the circumstances of their resolution remains incomplete. Here, we found that in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy, high intratumoral TLS density at the time of surgery is associated with pathologic response and improved relapse free survival. In areas of tumor regression, we further identified a non-canonical involuted morphology of TLS marked by dispersion of the B cell follicle, persistence of a T cell zone enriched for T cell-mature dendritic cell interactions, and increased expression of T cell memory markers. Collectively, these data suggest that TLS may serve be both a prognostic and predictive marker of response to immunotherapy in HCC and suggest a functional role for late-stage TLS T cell memory formation after elimination of viable tumor.
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| Overall design |
We utilized surgical resection specimens and peripheral blood obtained from patients with locally advanced hepatocellular carcinoma receiving neoadjuvant immune checkpoint blockade based therapy. Bulk RNA sequencing was performed on post-treatment tumor resection specimens to characterize differences in gene expression between tumors with high and low density of tertiary lymphoid structures. Tumor associated tertiary lymphoid structures were microdissected and subjected to bulk TCR and BCR sequencing using the Adaptive Biotechnologies ImmunoSEQ platform (shared separately). Single cell RNA, TCR, and BCR sequencing was performed on matched peripheral blood and tumor specimens to infer the identity of T and B cells identified in tertiary lymphoid structures.
*** Submitters state that raw data is being submitted to dbGap (phs003672.v1.p1)***
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| Contributor(s) |
Shu D, Yarchoan M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 16, 2024 |
| Last update date |
Sep 14, 2024 |
| Contact name |
Daniel H Shu |
| E-mail(s) |
daniel.shu@jhmi.edu
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| Organization name |
Johns Hopkins Sidney Kimmel Cancer Center
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| Department |
Oncology
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| Street address |
CRB1, RM 416, 1550 ORLEANS ST.
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| City |
BALTIMORE |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (14)
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| GSM8398966 |
P01, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398967 |
P02, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398968 |
P03, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398969 |
P07, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398970 |
P08, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398971 |
P11, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398972 |
P12, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398973 |
P13, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398974 |
P14, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398975 |
OT1, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398976 |
OT2, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398977 |
OT4, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398978 |
OT5, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
| GSM8398979 |
OT6, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires |
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| This SubSeries is part of SuperSeries: |
| GSE272348 |
Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade |
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| Relations |
| BioProject |
PRJNA1136492 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE272346_RAW.tar |
7.5 Mb |
(http)(custom) |
TAR (of TSV) |
| Raw data not provided for this record |
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