Abstract

   Small cell lung cancer (SCLC) is classified as a high-grade
   neuroendocrine (NE) tumor, but a subset of SCLC has been termed
   “variant” due to the loss of NE characteristics. In this study, we
   computed NE scores for patient-derived SCLC cell lines and xenografts,
   as well as human tumors. We aligned NE properties with transcription
   factor-defined molecular subtypes. Then we investigated the different
   immune phenotypes associated with high and low NE scores. We found
   repression of immune response genes as a shared feature between classic
   SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss
   of NE fate, variant SCLC tumors regain cell-autonomous immune gene
   expression and exhibit higher tumor-immune interactions. Pan-cancer
   analysis revealed this NE lineage-specific immune phenotype in other
   cancers. Additionally, we observed MHC I re-expression in SCLC upon
   development of chemoresistance. These findings may help guide the
   design of treatment regimens in SCLC.

   Subject terms: Small-cell lung cancer, Data mining
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   Ling Cai et al. used transcriptomic profiling data of healthy lung,
   patient-derived small cell lung cancer cell lines, xenografts, and
   primary tumors to examine a link between neuroendocrine (NE) signatures
   and immune gene expression. Their findings suggest that cell-autonomous
   immune gene repression is a shared feature between healthy and tumor
   cells of NE lineage and may influence tumor-immune cell interaction and
   response to immunotherapy.

Introduction

   Small cell lung cancer (SCLC), accounting for 15% of lung cancer cases,
   with a 5-year survival of 6%, is designated by the US Congress as a
   “recalcitrant cancer”^[82]1,[83]2. SCLC is classified as a high-grade
   neuroendocrine (NE) tumor^[84]3. A large fraction of SCLC tumors are
   driven by ASCL1, a lineage oncogene also important for pulmonary
   neuroendocrine cell (PNEC) fate determination^[85]4,[86]5. In healthy
   lung tissue, PNECs are rare and dormant^[87]6, whereas upon lung
   injury, some act as stem cells to regenerate surrounding epithelial
   cells^[88]7. SCLC occurs primarily in heavy smokers, but despite the
   very high mutation burden^[89]8–[90]10 from SCLC genomes predicted to
   contribute an ample supply of neoantigens, SCLCs express low levels of
   major histocompatibility complex class I (MHC I) proteins to present
   tumor-specific antigens^[91]11,[92]12. This could explain why, among
   various types of cancer, checkpoint-blockade immunotherapy
   underperforms in SCLC^[93]13,[94]14.

   Thirty-five years ago, it was observed that by contrast to classic SCLC
   cell lines (which grew in tissue culture as floating cell aggregates),
   a subset of patient-derived SCLC lines behaved differently—growing as
   adherent monolayers in culture, with morphologically larger cells, more
   prominent nucleoli, and expressed few or no NE markers^[95]15,[96]16.
   These characteristics led such tumors to be termed “variant” or
   “non-NE” SCLC. Many of these variant SCLC lines were established from
   patients whose tumors had acquired resistance to chemotherapy and
   clinically relapsed, a context in which genomic MYC amplification was
   also noted to be more frequent^[97]17. Notch activation had been shown
   to mediate the transition from classic to variant subtypes and accounts
   for the intratumoral heterogeneity commonly seen in SCLC^[98]18.

   Recently, extending the concepts of classic and variant SCLC, both
   intertumoral, and intratumoral heterogeneity in SCLC has been
   documented and has been associated with the expression of
   lineage-specific transcription factors (TFs) ASCL1, NEUROD1, YAP1, and
   POU2F3, and these various subtypes express different levels of NE
   markers^[99]19–[100]21.

   We have previously defined a 50-gene NE signature that helps us
   quantify the NE properties as a continuous NE score ranging from −1 to
   1, with a more positive score indicating higher NE properties^[101]22.
   In the current study, we applied this NE scoring method to SCLC samples
   from preclinical models and patient tumors. We first assessed the
   relationship between NE scores and SCLC molecular subtypes. Then, we
   investigated the immune phenotypes associated with variable NE scores
   in SCLC and other cancer types.

Results

Relationship between NE scores and SCLC molecular subtypes

   Using the 50-gene NE signature updated with all available SCLC-related
   RNA-seq data (Supplementary Data [102]1), we computed NE scores for
   patient-derived SCLC lines and xenografts (PDXs) as well as four
   independent patient tumor data sets (including one newly generated for
   this study) (Table [103]1 and Supplementary Data [104]2). We examined
   the relationship between NE scores and expression of SCLC molecular
   subtype-specific TFs as proposed by Rudin et al. (Fig. [105]1a, b). Our
   findings are largely consistent with the previous proposal that assigns
   ASCL1^+ and NEUROD1^+ SCLCs to NE subtypes and POU2F3^+ and
   YAP1^+ SCLCs to non-NE subtypes. However, we note some discrepancies.
   First, we found that while expression of ASCL1 and NEUROD1 seems to be
   mutually exclusive in cell lines, they seem to co-express in many of
   the tumor samples; a small set of samples with low NE scores still
   express ASCL1 or NEUROD1; in “George_2015”, “Jiang_2016” and our own
   data set, we have observed rare POU2F3^+ samples that have high NE
   scores.

Table 1.

   Data sets used for analyses.
   Source Name Tissue source Sample type n References