This article is more than 5 years old. Information may no longer be current.
Analysis identifies genetic mutations linked to SCLC tumor growth
Several members of the SOX family of genes were observed to be significantly mutated in small cell lung cancers, with evidence of amplification and overexpression in approximately 27% of collected samples, according to a comprehensive genomic analysis.
“Small cell lung cancers are very aggressive. Most are found late, when the cancer has spread and typical survival is less than a year after diagnosis,” Charles Rudin, MD, PhD, professor of oncology at the Johns Hopkins Kimmel Cancer Center, said in a press release. “Our genomic studies may help identify genetic pathways responsible for the disease and give us new ideas on developing drugs to treat it.”
Prior studies assessing the genetic alterations in SCLC tumors revealed high prevalence of inactivating mutations in TP53, RB1 and PTEN, rare activating mutations in PIK3CA, EGFR and KRAS8, amplification of MYC family members, EGFR and BCL2, and loss of RASSF1A, PTEN and FHIT.
To attain a better understanding of SCLC genomic changes, Rudin and colleagues applied next-generation sequencing technologies to characterize 80 human SCLCs, including 36 primary SCLC human tumor and adjacent normal sample pairs, and 17 paired SCLC cell lines and their patient-matched lymphoblastoid cell lines.
In addition, they characterized four primary SCLC tumors and 23 SCLC cell lines without matched normal controls.
According to study results, genomic mapping identified 22 significantly mutated genes in the SCLC samples, including genes encoding kinases, G protein–coupled receptors and chromatin-modifying proteins.
Comparing the observed mutations with those reported in COSMIC12 and a large-scale colon cancer mutation screen, the researchers identified an additional 150 “hotspot” mutations in 116 genes, including genes encoding Ras family regulators, chromatin-modifying enzymes or transcriptional regulators, ionotropic glutamate receptor, kinases, protein phosphatases and G protein–coupled receptors.
The researchers identified high levels of amplification (copy number of ≥4) of SOX2 in approximately 27% (15/56) of the SCLC samples. RNA-sequence data demonstrate that most of the SCLC samples, including those with SOX2 amplification, exhibited higher SOX2 expression vs. adjacent normal samples. The researchers further assessed SOX2 expression by immunohistochemistry and copy-number change by fluorescence in situ hybridization in an independent cohort of 110 primary SCLC tumor samples. Expression of SOX2 was strongly correlated with increased gene copy number and with clinical stage.
“Notably, conditional induction of SOX2 in lung epithelial cells is also known to increase the number of neural progenitor cells,” Rudin and colleagues wrote. “SCLCs are tumors with neuroendocrine features. SOX2 protein overexpression has previously been noted in high-grade SCLC, and immunoreactive antibodies against SOX2 have been detected in sera from SCLC patients. These observations, together with the frequent amplifications identified here, imply that SOX2 has an important role as a putative lineage-survival oncogene in SCLC.”
Disclosure: The researchers report employment relationships with Genentech and Leica Microsystems, as well as stockholder roles in Roche.
Perspective
Back to TopIt is well recognized that small cell lung cancer is strongly associated with cigarette smoking, almost exclusively. SCLC is also highly characteristic in its clinical phenotype, early metastasis, initial chemo- and radio-sensitivity with high response rates but subsequent resistant relapse, and a 2-year survival of <15%. A number of tumor suppressor genes are inactivated in SCLC, including TP53 (80%-90%), RB1 (60%-90%) and PTEN (13%). Less frequent activating mutations have been found in PIK3CA, EGFR and KRAS (all ≤10%; http://www.sanger.ac.uk/genetics/CGP/cosmic/). MYC is found to be amplified in about 20% of cases. To put in perspective, the first detailed and comprehensive genomic landscape of SCLC was reported in 2010 by Erin Pleasance and colleagues, revealing complex tobacco exposure signatures (Nature. 2010;463:184-190). In the study, a SOLiD massively parallel sequencing platform was used to sequence a SCLC cell line NCI-H209 to an estimated depth of coverage of about 30x, yielding 22,910 somatic substitutions that were identified, including 132 in coding exons. The study highlighted the finding of recurrent rearrangement of CDH7, a chromatin remodeller, in the disease as candidate driver genomic alteration in SCLC, raising its potential as therapeutic target in this deadly disease. Next-generation cancer genome sequencing (NGS) such as this illustrated the potential for the new sequencing technology to shed unprecedented insights into the cancer genome architecture and functionality in relation to the mutational processes, cellular repair pathways and gene networks within.
In just a short 2-year period, Charles Rudin and colleagues (Nat Genet. 2012;doi:10.1038/ng.2405) now reported another comprehensive genomic analysis of SCLC genome in which SOX2 was identified as a frequently amplified gene, validated to be often highly expressed in SCLC tumor tissues. In this most recent NGS study, this highly collaborative research group analyzed the cancer exome, transcriptome and also copy-number variations of samples from 36 primary SCLC with normal tissue pairs, and 17 matched SCLC and lymphoblastoid cell lines. Additional data from four primary tumors and 23 SCLC cell lines were also obtained. One SCLC tumor/normal paired sample set was also subjected to whole-genome sequencing analysis. They reported 22 significantly mutated genes, including kinase-encoding genes, G protein-coupled receptors and chromatin-modifying protein genes. Of particular interest, several SOX2 family member genes were found mutated, along with SOX2 genomic amplification in about 27% of the samples. Novel recurrent RLF-MYCL1 fusion was also identified in RNA-seq. Functional RNAi preclinical studies confirmed the proliferate role of SOX2 in SCLC.
Here, this study highlighted a few important points and lessons. First, NGS in cancer genome analysis has progressed rapidly in unprecedented pace. Fast dropping cost with time empowers its application and use in more cancer centers and more tumor samples, thus increasing the statistical and analytical strength of the studies. Second, highly collaborative NGS effort is feasible and the interest of studying SCLC has not been extinguished yet, despite the pitifully lack of advances in targeted therapy in this deadly disease over the last decade. Third, integrative genomic analysis utilizing whole-exomic and whole-transcriptomic sequencing adds great value in cancer genome interrogation. Certainly, the debate of relative cost-effectiveness and true values of adopting whole-genome sequencing over whole-exomic sequencing has not come to an end yet. Economic consideration aside, the level of bioinformatic analysis complexity remains a bottleneck in many centers nowadays. Inevitably, one would certainly expect to see more cancer genomes to be sequenced, more cancer genes to be discovered and, hopefully, more cancer drugs to be developed in the foreseeable future. It is comforting to witness lung cancer being in the forefront leading edge of the waves of NGS in advancing cancer genomic sciences in this highly lethal disease. Last, hopefully one need not be totally nihilistic about lung cancer any further, despite our collective treatment failures and lack of mortality impact in the past, whether it is smoker or nonsmoker lung cancer.
Collapse