Transcriptomic basis of sex loss in the pea aphid

BACKGROUND

Transitions from sexual to asexual reproduction are common in eukaryotes, but the underlying mechanisms remain poorly known. The pea aphid-Acyrthosiphon pisum-exhibits reproductive polymorphism, with cyclical parthenogenetic and obligate parthenogenetic lineages, offering an opportunity to decipher the genetic basis of sex loss. Previous work on this species identified a single 840 kb region controlling reproductive polymorphism and carrying 32 genes. With the aim of identifying the gene(s) responsible for sex loss and the resulting consequences on the genetic programs controlling sexual or asexual embryogenesis, we compared the transcriptomic response to photoperiod shortening-the main sex-inducing cue-of a sexual and an obligate asexual lineage of the pea aphid, focusing on heads (where the photoperiodic cue is detected) and embryos (the final target of the cue).

RESULTS

Our analyses revealed that four genes (one expressed in the head, and three in the embryos) of the region responded differently to photoperiod in the two lineages. We also found that the downstream genetic programs expressed during embryonic development of a future sexual female encompass ∼1600 genes, among which miRNAs, piRNAs and histone modification pathways are overrepresented. These genes mainly co-localize in two genomic regions enriched in transposable elements (TEs).

CONCLUSIONS

Our results suggest that the causal polymorphism(s) in the 840 kb region somehow impair downstream epigenetic and post-transcriptional regulations in obligate asexual lineages, thereby sustaining asexual reproduction.

Early macrophage response to obesity encompasses Interferon Regulatory Factor 5 regulated mitochondrial architecture remodelling

Adipose tissue macrophages (ATM) adapt to changes in their energetic microenvironment. Caloric excess, in a range from transient to diet-induced obesity, could result in the transition of ATMs from highly oxidative and protective to highly inflammatory and metabolically deleterious. Here, we demonstrate that Interferon Regulatory Factor 5 (IRF5) is a key regulator of macrophage oxidative capacity in response to caloric excess. ATMs from mice with genetic-deficiency of Irf5 are characterised by increased oxidative respiration and mitochondrial membrane potential. Transient inhibition of IRF5 activity leads to a similar respiratory phenotype as genomic deletion, and is reversible by reconstitution of IRF5 expression. We find that the highly oxidative nature of Irf5-deficient macrophages results from transcriptional de-repression of the mitochondrial matrix component Growth Hormone Inducible Transmembrane Protein (GHITM) gene. The Irf5-deficiency-associated high oxygen consumption could be alleviated by experimental suppression of Ghitm expression. ATMs and monocytes from patients with obesity or with type-2 diabetes retain the reciprocal regulatory relationship between Irf5 and Ghitm. Thus, our study provides insights into the mechanism of how the inflammatory transcription factor IRF5 controls physiological adaptation to diet-induced obesity via regulating mitochondrial architecture in macrophages.

Interferon Regulatory Factor 5 levels have been shown to increase in adipose tissue macrophages in diet-induced obesity. Here authors show that IRF5 transcriptionally represses the Growth Hormone Inducible Transmembrane Protein gene encoding a mitochondrial protein important for oxidative respiration in macrophages, thus driving the detrimental metabolic changes observed in obesity.

Prognostic value of tumor mutational burden in patients with oral cavity squamous cell carcinoma treated with upfront surgery

Background

Oral cavity is the most prevalent site of head and neck squamous cell carcinomas (HNSCCs). Most often diagnosed at a locally advanced stage, treatment is multimodal with surgery as the cornerstone. The aim of this study was to explore the molecular landscape of a homogenous cohort of oral cavity squamous cell carcinomas (OCSCCs), and to assess the prognostic value of tumor mutational burden (TMB), along with classical molecular and clinical parameters.

Patients and methods

One hundred and fifty-one consecutive patients with OCSCC treated with upfront surgery at the Institut Curie were analyzed. Sequencing of tumor DNA from frozen specimens was carried out using an in-house targeted next-generation sequencing panel (571 genes). The impact of molecular alterations and TMB on disease-free survival (DFS) and overall survival (OS) was evaluated in univariate and multivariate analyses.

Results

Pathological tumor stage, extranodal spread, vascular emboli, and perineural invasion were associated with both DFS and OS. TP53 was the most mutated gene (71%). Other frequent molecular alterations included the TERT promoter (50%), CDKN2A (25%), FAT1 (17%), PIK3CA (14%), and NOTCH1 (15%) genes. Transforming growth factor-β pathway alterations (4%) were associated with poor OS (P = 0.01) and DFS (P = 0.02) in univariate and multivariate analyses. High TMB was associated with prolonged OS (P = 0.01 and P = 0.02, in the highest 10% and 20% TMB values, respectively), but not with DFS. Correlation of TMB with OS remained significant in multivariate analysis (P = 0.01 and P = 0.005 in the highest 10% and 20% TMB values, respectively). Pathological tumor stage combined with high TMB was associated with good prognosis.

Conclusion

Our results suggest that a high TMB is associated with a favorable prognosis in patients with OCSCC treated with upfront surgery.

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High TMB is associated with a favorable prognosis in patients with OCSCC treated with upfront surgery

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Pathological tumor stage combined with high TMB is associated with good prognosis

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TP53 was the most mutated gene (71%). Other frequent molecular alterations included the TERT promoter (50%)

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TGFβ pathway alterations were associated with poor outcomes, although it was only observed in 4% of the patients

Abstract PD1-06: Comparison of mutational landscapes of primary breast cancer and first metastatic relapse: Results from the ESOPE study

Background

Genomic profile of breast cancer metastases (M) may differ from that of the primary tumor (PT). In a multicenter prospective study (ESOPE, NCT 01956552) including 130 patients with biopsies of the first metastatic deposit, we have shown that luminal breast cancers are the most prone to phenotypical subtype changes (Comte et al, ASCO 2016#550). We report here the first results of a comparative PT/M targeted next generation sequencing (NGS) mutational analysis.

Methods

Of 130 patients, 117 paired PT/M samples obtained before any treatment were available for analysis. Targeted Sequencing was done using Illumina Hiseq2500 technology with a custom made 95 breast cancer associated genes panel. Sequence data were aligned to the human reference genome (hg19) using Bowtie2 algorithm. Median depth was 607X and 87% of targets achieved 100X depth. SNVs and indels were called using GATK UnifiedGenotyper. We retained COSMIC confirmed non synonymous, exonic/splice variants and observed at a frequency lower than 0,1% in population. Further confirmation of detected variants was performed with comparison to public databases (cbioportal, tumorportal), and potential pathogenicity was evaluated with 4 different public algorithms. We present here the results obtained from the first 35 matched PT/M samples (liver mets 68%), focusing analysis on 40 genes including PIK3CA (20 genes), ER (6 genes) and MAPK (11 genes) pathways, RUNX1, CDH1 and TP53 genes.

Results

Patients characteristics are representative of patients with first line metastatic breast cancer (Comte et al, ASCO 2016#550). Among the 40 genes analyzed in the 70 samples, we detected 134 somatic mutations (70 in PT and 64 in M) including 15 indels and 119 SNV. Among these 134 mutations there were 74 different mutations (66SNV and 8 indels) classified pathogenic for 26 and of unknown pathogenicity for 48 of them. We detected at least 1 mutation in 31 PT and in 28 M. Median numbers of mutations were 1 in PT (range 1-9) and 1 in M (range1-22) samples (p=0.295, Wilcoxon rank sum test). Top ten mutated genes in PT included PIK3CA, TP53, NCOR1, NF1, GATA3, CDH1, ERBB3, PTEN, HRAS, INPP4B. In M samples, the 10 top genes were PIK3CA, TP53, ERBB3, AKT3, CDH1, ERBB4, GATA3, INPP4B, MET, MTOR. Only 3 ESR1 mutations were detected, including 1 PT/M pair and 1 M. Beyond highly shared PIK3CA and TP53 mutations, overall crude PT/M discordance rate was 31%. Analysis by histological subtypes showed PT and M specific mutational profiles, suggesting a role in ERB gene family (notably ERBB3) and MAPK driven pathways in early metastatic progression. Specific metastatic site analysis suggested enrichment in MAPK pathway mutations in liver metastases when compared to other sites. Variant allelic fractions were globally not significantly different between PT and M samples.

Conclusion

In this prospective multicenter series of systematic biopsies of first metastases, we report a targeted mutational analysis of matched PT and M samples not modified by previous therapy exposure. Early analyses suggest specific genotypical changes according to tumor subtype and/or metastatic site. Extended and updated results will be reported at the meeting.

Citation Format: Cottu PH, Boulai A, Callens C, Baulande S, Legoix-Ne P, Bernard V, Vincent-Salomon A, Benhamo V, Brain EGC, Chemlali W, Campone M, Bachelot TD, Giacchetti S, Bonneterre J, Bidard F-C, Servois V, Comte A, Belin L, Sigal B, Bièche I. Comparison of mutational landscapes of primary breast cancer and first metastatic relapse: Results from the ESOPE study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD1-06.

Adiponutrin, a transmembrane protein corresponding to a novel dietary- and obesity-linked mRNA specifically expressed in the adipose lineage

We have used a mRNA differential display technique to identify new genes involved in the reprogramming of gene expression during the adipose conversion of mouse 3T3 preadipocyte cell lines. We report here on the identification and cloning of a novel adipose-specific cDNA encoding a predicted membrane protein of 413 amino acids. The level of the corresponding 3.2-kilobase mRNA is tremendously increased during 3T3-L1 and 3T3-F442A differentiation into adipocytes. A single, very abundant 3.2-kilobase transcript is also found in inguinal and epididymal white adipose tissues and in interscapular brown adipose tissue but not in any other tissues examined. Its expression in adipose tissue is under tight nutritional regulation. The level of this novel 3.2-kilobase transcript becomes virtually nondetectable during fasting but is dramatically increased when fasted mice are refed a high carbohydrate diet. Based on its adipose specificity and dietary regulation, the novel gene product has been designated adiponutrin. The expression of adiponutrin mRNA is also 50-fold elevated in genetically obese fa/fa rats, indicating a link between adiponutrin and obesity. Western blot and confocal imagery analyses with epitope-tagged protein transiently expressed in 3T3-L1 adipocytes, and COS cells show that adiponutrin strictly localizes to membranes and is absent from the cytosol. Sequence analysis reveals homologies with several other members of related eukaryotic proteins, including a human paralog, which has been recently described in vesicular transport mechanisms. This leads us to suggest that adiponutrin could be involved in vesicular targeting and protein transport restricted to the adipocyte function.

An element within the 5' untranslated region of human Hsp70 mRNA which acts as a general enhancer of mRNA translation

The untranslated regions of mRNAs encoding heat-shock proteins have been reported to contain elements important to the post-transcriptional regulation of these key components of the stress response. In this report we describe an element from the 5'UTR of human Hsp70 mRNA that increases the efficiency of mRNA translation. Cloning of this region upstream of the coding sequence of two different reporter genes (firefly luciferase and chloramphenicol acetyltransferase) increases expression of the reporter under normal cell culture conditions by up to an order of magnitude. This effect was observed in three different promoter contexts (HSP, SV40 and CMV) and in six cell lines. The increase in protein production is not accompanied by any alteration in mRNA levels, suggesting that the element facilitates translation. 5' or 3' truncated sequences are ineffective in enhancing reporter expression, suggesting that the activity arises from the secondary structure of the element, rather than from some smaller defined motif. Computer analysis of this region revealed that it is able to form stable secondary structures (DeltaG approximately -292.6 kJ x mol(-1)). The Hsp70 element does not seem to act as an internal ribosome entry site. Incorporation of the sequence into plasmids used for DNA vaccination produces increased antibody responses, confirming that the sequence is functional in primary cells. These data suggest that the 5'UTR of human Hsp70 mRNA plays an important role in determining Hsp70 expression levels, and that it contains an element of general utility in enhancing recombinant protein expression systems.