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Tumor Discovery HRD genomic alterations in Chinese NSCLC

Despite these advances, studies specifically addressing (LUAD or LUSC); (iii) availability of sufficient formalin-
the clinical and molecular landscape of HRD in NSCLC, fixed paraffin-embedded (FFPE) tumor tissue for DNA
particularly in East Asian populations, remain scarce. Most extraction, with tumor cellularity >30%; (iv) availability
large-scale HRD studies have focused on breast, ovarian, of matched germline peripheral blood samples; (v) ability
and prostate cancers, where HRD is more prevalent and to provide written informed consent; and (vi) complete
its prognostic and predictive value is well established. In clinicopathological and demographic data.
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NSCLC, the prevalence, clinical significance, and biomarker The exclusion criteria are as follows: (i) prior
potential of HRD, especially the commonly mutated genes neoadjuvant chemotherapy, radiotherapy, or targeted
such as EGFR, TP53, and ALK are not well characterized, therapy before tissue sampling, to avoid treatment-induced
and evidence from Chinese populations is particularly genomic alterations; (ii) insufficient tumor cellularity
limited. At present, the mainstream HRD score is based (<30%) in FFPE samples; (iii) poor DNA quality or quantity
on the Food and Drug Administration-approved Myriad after extraction; (iv) diagnosis of small cell lung cancer or
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HRD assay, which uses a threshold of 42. In this study, other rare NSCLC subtypes; and (v) presence of medical
the HRD threshold was set at 43, determined according or psychiatric conditions that precluded the possibility of
to the genomic database of the Chinese population. This obtaining informed consent.
threshold better reflects the practical value of our research
in Asian NSCLC patients. These criteria were established to ensure high-quality
genomic data and accurate HRD assessment and to
In addition, evidence has shown that cancers with reduce confounding factors that could artificially alter the
HRD exhibit enhanced immunogenicity, and checkpoint observed HRD-related mutation frequency. By excluding
inhibitors demonstrate potential efficacy. Numerous patients with prior systemic therapy, inadequate tissue or
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oncological studies have illustrated the potential of HRD DNA, or inability to provide informed consent, we aimed
as a biomarker for immunotherapy. 30,31 One previous to capture the true prevalence of HRD-related mutations in
study observed the disparities in PD-L1 expression status, treatment-naïve, representative Chinese NSCLC patients.
genetic backgrounds, and exposure to the environment Informed consent was obtained from all patients, and the
between Asia and the United States. Thus, there is a study protocol was approved by the institutional ethical
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need for region-specific research on the applicability and review committee.
predictive/prognostic values of HRD. Further investigation
into HRD could be crucial for identifying new therapeutic 2.2. DNA extraction and quality control
targets in NSCLC.
Total genomic DNA from FFPE tumor tissues was isolated
In this study, we aim to describe the correlation between using the Paraffin-Embedded Tissue DNA Extraction
HRD scores and clinical characteristics in Chinese patients Kit (centrifugal column method) from Novogene
with NSCLC, as well as the mutation status in HRD- Biotechnology, Tianjin, China; it is a modified protocol
related genes. Furthermore, we attempted to analyze the of a standard DNA extraction kit that provides high yield
relationship between HRD scores and PD-L1 expression, and quality of purified DNA from the fragmented genomic
providing foundational data for selecting biomarkers in DNA from FFPE samples. For germline DNA, leukocyte
future clinical targeted therapies for NSCLC. from the peripheral blood sample was used, and the DNA
was extracted using the Tienken Blood DNA kit of Tiangen
2. Materials and methods Biotech, Beijing, China. DNA yield and quality were
2.1. Patient cohort and sample collection determined by using a Qubit Fluorometer (Thermo Fisher
Scientific, Waltham, USA) and Agilent 2,100 Bioanalyzer
This study is a retrospective study conducted on 158 (Agilent Technologies, Santa Clara, USA).
pathologically proven NSCLC patients treated at the
Chongqing University Three Gorges Hospital. The cohort 2.3. Gene panel design and sequencing
included 148 patients with LUAD and 10 patients with Targeted next-generation sequencing (NGS) was done on
LUSC, which are the two most common subtypes of a DNAseq custom hybrid capture panel consisting of 188
NSCLC. cancer genes and 37,000 genome-wide single nucleotide
Patients were enrolled consecutively according to polymorphism (SNP) markers. This panel was selectively
the order of their thoracic surgery admissions over a used to detect somatic and germline mutations in the
6-month period, from August 2023 to January 2024. The genes related to HRR and to assess the HRD score based
inclusion criteria are as follows: (i) age between 18 and on genomic instability. The panel includes comprehensive
75 years; (ii) histologically confirmed diagnosis of NSCLC coverage of EGFR mutation hotspots and other driver

Volume 4 Issue 3 (2025) 34 doi: 10.36922/TD025180032