A patent-based analysis of the evolution of basic, mission-oriented, and applied research in European universities

The dynamics of basic and applied research at university and industry have steadily changed since the Eighties, with the private sector reducing its investments in science and universities experiencing significant remodelling in the governance of their funding. While studies have focussed on documenting these changes in industry, less attention has been paid to observe the trajectories of basic and applied research in universities. This work contributes to fill this gap by looking at the evolution of publicly funded research that has been patented by universities between 1978 and 2015. First, we adopt a critical perspective of the basic versus applied dichotomy and identify patents according to three typologies of research: basic, mission-oriented, and applied research. Second, we describe the evolution of these three typologies in universities compared to industry. Our results show that over the years, patents from academic research that was publicly funded have become more oriented towards pure basic research, with mission-oriented basic research and pure applied research decreasing from the late 1990s. These results complement and extend the literature on basic and applied research dynamics in the private sector. By introducing mission-oriented research as a type of basic research with consideration of use, the work problematises the basic and applied research dichotomy and provides insights into the evolution of academic research focus, offering a more complex picture of how university research contributes to industry and broader social value creation.

Pregnancy-associated plasma protein A mRNA expression as a marker for differentiated thyroid cancer: results from a "surgical" and a "cytological" series

PURPOSE

Pregnancy-associated plasma protein A (PAPPA) is a metalloproteinase initially described for its role during pregnancy. PAPPA regulates IGF ligands 1 (IGF1) bioavailability through the degradation of IGF-binding protein 4 (IGFBP4). After the cleavage of IGFBP4, free IGF1 is able to bind IGF1 receptors (IGF1R) triggering the downstream signaling. Recently, PAPPA expression has been linked with development of several cancers. No data have been published on thyroid cancer, yet.

METHODS

We evaluated PAPPA, insulin-like growth factor (IGF1), IGF1 receptors (IGF1R) and IGF-binding protein 4 (IGFBP4) mRNA expression levels in a "Surgical series" of 94 thyroid nodules (64 cancers, 16 follicular adenomas and 14 hyperplastic nodules) and in a "Cytological series" of 80 nodules from 74 patients underwent to fine-needle aspiration cytology (FNAC). In tissues, PAPPA was also evaluated by western blot.

RESULTS

We found that PAPPA expression was increased in thyroid cancer specimen at mRNA and protein levels and that, adenomas and hyperplastic nodules had an expression similar to normal tissues. When applied on thyroid cytologies, PAPPA expression was able to discriminate benign from malignant nodules contributing to pre-surgical classification of the nodules. We calculated a cut-off with a good specificity (91%) which reached 100% when combined with molecular biology.

CONCLUSION

These results show that PAPPA could represent a promising diagnostic marker for differentiated thyroid cancer.

Thr92Ala polymorphism in the type 2 deiodinase gene: an evolutionary perspective

PURPOSE

In the past, a role of thyroid hormones in human evolution has been hypothesized. T3, the metabolically active form, derives from extrathyroidal conversion of T4 by deionidase 2 (D2) enzyme encoded by DIO2 gene. In thyroid-deficient patients, decreased levels of free T3 have been associated with the polymorphism rs225014 A/G in DIO2, which causes the substitution of Threonine with Alanine (p.Thr92Ala) at protein level.

METHODS

We compared DNA and protein sequences of D2 from archaic human subspecies with those of contemporary humans.

RESULTS

Neanderthals and Denisovans displayed only the G allele at the rs225014 polymorphism, which encodes for an Alanine on the amino acid level. These data suggest that these hominines were homozygous for the Ala amino acid. These arcaic humans often lived in condition of iodine deficiency and thus, defective mechanisms of T3 biosynthesis could be life threatining. A reduced D2 activity is likely to cause decreased T3 levels, which could be critical for those individuals. Neanderthals and Denisovans were hunters/gatherers, and their diet was mainly based on the consumption of meat, with a low intake of carbohydrates. The need for circulating T3 is reduced at such alimentary conditions. On the basis of our genome comparisons the A allele, corresponding to Threonine and associated with higher levels of circulating T3 in thyroid-deficient patients, appeared for the first time during evolution in Anatomically Modern Humans during the Upper Pleistocene and has been conserved during the Neolithic age. With the advent of agriculture and herding, individuals carrying A allele might have a higher probability for surviving and reproducing. Thus, the variant was positively selected during the evolution.

CONCLUSION

Here we present an evolutionary perspective for p.Thr92Ala variant of D2 from Neanderthals to Anatomically Modern Humans.

Variants in MCT10 protein do not affect FT3 levels in athyreotic patients

PURPOSE

Several single-nucleotide polymorphisms in genes encoding for transporters have been associated with serum thyroid hormone concentrations with inconsistent results. The aim of this study was to assess the clinical significance of the rs17606253 in SLC16A10 gene alone and in combination with the DIO2 Thr92Ala variation in athyreotic patients.

METHODS

One-hundred patients submitted to total thyroidectomy and treated with levothyroxine were included. Pre- and post surgical serum TSH levels did not differ by more than ± 0.5 mIU/l.

RESULTS

Both patients carrying the wild-type allele or heterozygous for rs17606253 in SLC16A10 gene had a significant reduction in FT3 post surgical levels (p = 0.01 and p < 0.0001, respectively) while Thr92Ala in DIO2 gene was associated with reduced FT3 levels for heterozygous and rare homozygous patients (p < 0.0001 and p = 0.01, respectively). We identified two groups ("FT3 unchanged" and "FT3 reduced") using a cutoff of at least 0.5 pg/ml as a significant variation between pre- and post surgical FT3 values. In this case, the rs17606253 was not statistically associated with reduced FT3 levels at genotype and allele levels. On the contrary, the Thr92Ala in DIO2 gene was confirmed statistically associated with reduced FT3 levels after surgery with a p = 0.035 at genotype level and p = 0.014 at allele level.

CONCLUSIONS

We confirmed the role of DIO2 Thr92Ala polymorphism on T3 levels. On the contrary, SLC16A1 rs17606253 polymorphism did not impair hormone levels in athyreotic patients treated with levothyroxine therapy.

MicroRNA expression profile of thyroid nodules in fine-needle aspiration cytology: a confirmatory series

INTRODUCTION

MiRNAs are small endogenous non-coding RNAs implicated with gene expression regulation. Changes in miRNA levels have been reported in thyroid cancer. Fine-needle aspiration cytology (FNAC) is the most reliable tool for differential diagnosis of thyroid nodules.

METHODS

We have analyzed 174 FNAC from 168 patients with thyroid nodules for expression levels of 11 miRNAs (miRNA197; -187; -181b-3p; -181b-5p; -224; -181a; 146b; -221; -222; -155 and miRNA183) known to be up-regulated in cancer tissues compared to benign lesions. Expression of miRNAs was analyzed in FNA samples calculating the fold change of miRNA expression relative to normal thyroid tissue after normalization to an endogenous control.

RESULTS

In FNAC, miRNA expression was confirmed to be higher in malignant or suspicious for malignancy nodules compared to benign, only for miRNA146b, -222 and -221 (fold change expression ≥ 5).

CONCLUSION

In this study, we confirmed that a limited set of miRNAs can be used for the differential diagnosis of thyroid nodules.

HABP2 G534E variation in familial non-medullary thyroid cancer: an Italian series

INTRODUCTION

Thyroid cancer may have a familial predisposition and may occur in the context of hereditary syndromes or as isolated tumor. Recently, the G534E variant in the HABP2 gene has been suggested as causative mutation for familial thyroid cancer, but other studies gave contradictory results.

METHODS

We have analyzed the G534E variant in an Italian series of 63 familial thyroid cancer patients and 41 unaffected family members with end-point PCR, DHPLC and direct sequencing.

RESULTS

All samples analyzed displayed a pattern typical of the homozygous wild type revealing the absence of the G534E variant.

CONCLUSION

In this study, HABP2 G534E variant is not correlated with the familial form of PTC.

Identification of a SUFU germline mutation in a family with Gorlin syndrome

Gorlin syndrome (GS) is inherited in an autosomal dominant pattern with high-penetrance and is characterized by a range of developmental anomalies and increased risk of developing basal cell carcinoma and medulloblastoma. Between 50% and 85% of patients with GS harbor germ line mutations in the only susceptibility gene identified to date, PTCH1, a key component in the Sonic Hedgehog signaling pathway. Another component in this pathway, SUFU, is known to be involved in susceptibility to medulloblastoma but has never been reported in GS patients to date. We have identified the known c.1022 + 1G>A SUFU germ line splicing mutation in a family that was PTCH1-negative and who had signs and symptoms of GS, including medulloblastoma. This is the first report of a germ line SUFU mutation associated with GS.