Correlation of mesothelin (MSLN) expression measured by RNA sequencing (RNASeq) and immunohistochemistry (IHC) in MSLN-expressing tumors.
Authors: Hecht Joel R , Grierson Patrick , Welling Theodore H. , Spencer Kristen Renee , Hazim Antonious Ziad , Park Jong Chul , Ulrickson Matthew , Kirtane Kedar , Murthy Hemant S. , Patel Sandip Pravin , Specht Jennifer M. , Weng Wen-Kai , Maus Marcela Valderrama , Maloney David G. , Ng Eric Wai-Choi , Molina Julian R. , Mardiros Armen , Morelli Maria Pia , Welch John Sutton , Simeone Diane M. 
Published: January 2025

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Background:
BASECAMP-1 (NCT04981119) is a pre-screening study to identify patients with tumor-associated human leukocyte antigen (HLA)-A*02 loss of heterozygosity (LOH) for interventional studies, such as EVEREST-2 (NCT06051695), a phase 1/2 study of logic-gated chimeric antigen receptor T-cell (CAR T) therapy for MSLN-expressing cancers. MSLN is a cell surface protein expressed in several cancer types, including mesothelioma (MESO), colorectal (CRC), non-small cell lung (NSCLC), ovarian (OVCA), and pancreatic (PANC) cancer, which can be associated with poor prognosis (1). Longitudinal clinical, genomic, and biomarker data were collected from patients enrolled in BASECAMP-1, providing a large dataset for translational discovery and propensity scoring. The aim of this analysis was to determine whether MSLN expression measured by RNAseq and IHC are correlated among patients with solid tumors.
Methods:
In BASECAMP-1, tumor tissue from patients with germline heterozygous HLA-A*02 is tested for HLA-A*02 LOH using an investigational next generation sequencing device codeveloped with Tempus Labs (Lozac'hmeur, et al.
NPJ Precis Oncol.
2024) that detects somatic alterations, including HLA LOH, and generates RNAseq data (eg, MSLN expression). Gene-level transcripts per million read (TPM) values were determined and the log2 TPM +1 was displayed in a scatter plot (the mean and standard deviation [SD] are provided in the Table). Patients with HLA-A*02 LOH also submit tissue for IHC testing for exploratory biomarkers (eg, MSLN expression using anti-MSLN clone 5B2). Statistical significance was determined with ANOVA or t-tests.
Results:
As of June 1, 2024, 314 patients had been screened for BASECAMP-1 and had RNAseq results; 34 patients also had MSLN IHC results. MSLN expression by RNAseq was consistently higher in patients with PANC or OVCA vs CRC or NSCLC (
P
<0.001). MSLN expression by RNAseq and IHC were correlated overall (
P
<0.001), particularly among patients with PANC and OVCA. Among the 8 patients with OVCA or PANC who were IHC+ for MSLN, only 1 had an RNAseq value below 6 log2 TPM+1; this patient had mesonephric-like ovarian adenocarcinoma, which may account for the low value. The one MESO sample with both RNAseq and IHC available was IHC+ and had a high RNAseq value.
Conclusions:
This analysis demonstrated high correlation between RNAseq and IHC MSLN expression in tumor tissue. 1. Faust, et al.
Cancers.
2022.
Clinical trial information: NCT04981119
.

MSLN expression by RNASeq by tumor type and IHC status.

Tumor
Overall (N=314)
IHC data available (n=34)

MSLN Positive

MSLN Negative

n

Mean TPM

a

(SD)

n

Mean TPM

a

(SD)

n

Mean TPM

a

(SD)

All
314
5.1 (2.3)
20
6.0 (2.1)
14
2.3 (1.7)

adNSCLC
33
3.8 (2.4)
2
4.7 (1.7)
7
1.5 (1.3)

sqNSCLC
4
3.1 (1.8)
0

0

MESO
4
4.5 (4.2)
1
5.7
0

CRC
148
4.4 (2.0)
8
5.1 (2.1)
7
3.1 (1.6)

PANC
100
6.1 (1.8)
3
7.8 (0.6)
0

OVCA
25
7.2 (2.1)
5
6.6 (2.8)
0

a

MSLN log2 transcripts per million+1.

ad, adenocarcinoma; sq, squamous.