Page 30 - Read Online

David. J Cancer Metastasis Treat 2022;8:32 https://dx.doi.org/10.20517/2394-4722.2022.71 Page 3 of 12

tumor types [15,16] . Basal-like tumors largely corresponded to the QM-PDA subtype defined in the earlier
study, although these authors presented evidence that some of the mesenchymal gene expression in the
Collison classifier was derived from the stroma. In addition to tumor-specific gene expression subtypes,
these authors also identified two distinct stromal subtypes, normal or activated. The normal stromal subtype
was enriched with gene expression characteristic of pancreatic stellate cells, while the activated subtype
showed more diverse gene expression, mainly connected with macrophage-enriched genes. Importantly,
both classical and basal-like tumor cell gene expression was found among both stromal subtypes, arguing
against a causal connection between stromal and tumor gene expression.

A third study by Bailey et al. combined gene expression profiling with a comprehensive genomic analysis
(whole genome, exome and copy number analysis), all performed using bulk tumor samples with high
[17]
(> 40%) tumor cellularity . These authors identified four subtypes using RNA-seq: squamous, aberrantly
differentiated exocrine, pancreatic progenitor, and immunogenic. The squamous and pancreatic progenitor
subtypes corresponded well to the previously described QM-PDA/basal-like and classical subtypes,
respectively. Not surprisingly, tumors of the squamous subtype were more frequently associated with
adenosquamous histology, a long-observed subset of PDA tumors comprising up to 4% of PDA [18,19] ,
although not all tumors of the squamous subtype displayed this histology . Immunogenic tumors were
[17]
characterized by increased B and T cell infiltration, a characteristic captured due to the inclusion of stroma
in the samples used, while the tumor cell gene expression in the immunogenic subtype corresponded most
closely to the classical subtype.

Subsequent studies have supported the conclusions of Moffitt et al. arguing for the existence of two main
gene expression states within the tumor epithelium: classical and basal-like . Examination of sample
[16]
histology has suggested that the previously proposed exocrine/ADEX and immunogenic subtypes reflect
normal or stromal contamination, respectively [20-22] . Importantly, careful experimental microdissection
validated the conclusions based on the “digital” microdissection performed by Moffitt et al. Recent work has
suggested further refinement of the classical/basal-like dichotomy, suggesting that the basal-like and
classical categories can each be further broken down into A and B subtypes [16,22,23] . Additionally, a set of
“hybrid” tumors expressing genes of both subtypes were identified, suggesting the possibility that some
tumors harbor a mixture of basal-like and classical cells, or that individual cells may simultaneously express
both transcriptional programs. Single cell studies have indeed borne out both possibilities, identifying
tumors containing individual cells that were fully basal-like or classical , and also a subset of tumor cells
[23]
that indeed express genes of both programs simultaneously .
[24]
One of the most robust findings in all subtyping studies has been the poor survival of patients with basal-
like tumors in comparison with classical tumors. Several observations suggest more aggressive behavior by
basal-like tumors. For example, patient-derived xenografts (PDX) of a basal-like phenotype grew
considerably faster than PDX tumors of a classical phenotype . Until recently, most pancreatic tumor
[16]
samples used for subtyping studies have been material obtained from surgically resected samples, skewing
sample representation towards the ~15% of relatively early-stage tumors that are eligible for surgical
resection. Recently, the COMPASS trial has made available samples from late-stage patients not eligible for
surgery, making their primary tumors and metastases available for subtyping. This allowed examination of
subtype representation at various stages of tumor progression. This showed that basal-like cancers are more
highly represented in tumors from Stage IV patients compared to those with resectable Stage I/II tumors
(36% vs. 14%), suggesting that studies reliant only on resected tumors may underestimate the frequency of
[23]
basal-like tumors .