Michael D. Waterfield.

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The mitochondrial protese HtrA2 is regulated by Parkinson's disease-associated kinase PINK1

The mitochondrial protese HtrA2 is regulated by Parkinson's disease-associated kinase PINK

<i>KRAS</i> mutations observed in human NSCLC in order of decreasing frequency (http://www.sanger.co.uk/cosmic; accessed 14^th July 2015).

<p><i>KRAS</i> mutations observed in human NSCLC in order of decreasing frequency (<a href="http://www.sanger.co.uk/cosmic" target="_blank">http://www.sanger.co.uk/cosmic</a>; accessed 14^th July 2015).</p

Correlation of NGS <i>KRAS</i> mutant allele frequency with digital PCR <i>KRAS</i> mutant allele frequency detected in the appropriate multiplex assay for FFPE tissue DNA and cell line gDNA samples.

<p>Correlation of NGS <i>KRAS</i> mutant allele frequency with digital PCR <i>KRAS</i> mutant allele frequency detected in the appropriate multiplex assay for FFPE tissue DNA and cell line gDNA samples.</p

<i>KRAS</i> mutant FFPE tissue DNA analysis using multiplex and duplex assays to detect <i>KRAS</i> mutant clones.

<p>All samples, except for S011, were analysed with multiplexes A, B and C (upper panels) and the <i>KRAS</i> mutation detected was subsequently confirmed with the appropriate duplex assay (lower panels). Mutant DNA droplet populations are highlighted with a red dashed square. Droplet populations caused by cross-reactivity with a <i>KRAS</i> mutant DNA species not present in the multiplex are indicated by a yellow dashed square.</p

<i>KRAS</i> multiplex digital PCR assays A-C and corresponding duplex assays.

<p>Multiplex A (top left panel) is an assay combination of 900 nM primers and 500 nM G13C probe (red dashed square), 450 nM primers and 250 nM G12C probe (blue dashed square) and 225 nM primers and 125 nM G12V probe (yellow dashed square). Multiplex B (top middle panel) is an assay combination of 675 nM primers and 375 nM G12S probe (red dashed square), 450 nM primers and 250 nM G12D probe (blue dashed square) and 225 nM primers and 125 nM G13D probe (yellow dashed square). Multiplex C (top right panel) is an assay combination of 675 nM primers and 375 nM G12R probe (red dashed square), 450 nM primers and 250 nM G12A probe (blue dashed square) and 900 nM primers and 500 nM Q61H probe (yellow dashed square). Multiplex C has 900 nM primers and 500 nM Q61H wild-type probe in addition to a G12C wild-type assay. All other wild-type droplet populations shown, except in the Q61H duplex assay, are 450 nM primers and 250 nM G12C wild-type probe. All panels in the left and centre columns show a FAM amplitude up to 18000 and an HEX amplitude up to 6000. Panels in the right column have a FAM amplitude up to 18000 and a HEX amplitude up to 11000.</p

<i>KRAS</i> duplex assays at optimal annealing temperature.

<p>Droplet populations observed for each duplex assay tested with wild-type and relevant mutant cell line gDNA or oligonucleotide at the optimal annealing temperature e.g. G12V panel top left shows droplet populations seen with WT for G12V assay, G12V assay, NCI-H727 gDNA and NCI-H1975 gDNA present. HEX amplitude is up to 6000 on the x axis and FAM amplitude up to 11000 on the y-axis of each panel. Key: Black drops- empty droplets, blue- mutant DNA FAM positive droplets, green- wild-type DNA HEX positive droplets, brown—wild-type and mutant DNA double positive droplets.</p

<i>KRAS</i> mutations observed in human cancer in order of decreasing frequency (http://www.sanger.co.uk/cosmic; accessed 14^th July 2015).

<p><i>KRAS</i> mutations observed in human cancer in order of decreasing frequency (<a href="http://www.sanger.co.uk/cosmic" target="_blank">http://www.sanger.co.uk/cosmic</a>; accessed 14^th July 2015).</p

Antibodies against endogenous retroviruses promote lung cancer immunotherapy.

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)1,2. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive1,2. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma3. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response