The next-generation Open Targets Platform: reimagined, redesigned, rebuilt.

The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data. Since our last update, we have reimagined, redesigned, and rebuilt the Platform in order to streamline data integration and harmonisation, expand the ways in which users can explore the data, and improve the user experience. The gene-disease causal evidence has been enhanced and expanded to better capture disease causality across rare, common, and somatic diseases. For target and drug annotations, we have incorporated new features that help assess target safety and tractability, including genetic constraint, PROTACtability assessments, and AlphaFold structure predictions. We have also introduced new machine learning applications for knowledge extraction from the published literature, clinical trial information, and drug labels. The new technologies and frameworks introduced since the last update will ease the introduction of new features and the creation of separate instances of the Platform adapted to user requirements. Our new Community forum, expanded training materials, and outreach programme support our users in a range of use cases.

Prevalence of pathogenic germline variants in patients with metastatic renal cell carcinoma.

PURPOSE: Germline pathogenic variants are estimated to affect 3-5% of renal cell carcinoma (RCC) patients. However, higher mutational prevalence in non-clear cell RCC (non-ccRCC) and advanced disease has been suggested. METHODS: To clarify the prevalence of pathogenic germline variants in metastatic RCC, we sequenced 29 cancer susceptibility genes in 294 unselected metastatic RCC cases plus 21 patients with clinical hereditary features. In 145 tumors, genes frequently mutated in RCC were sequenced and methylation was assessed in selected cases. RESULTS: Germline variants in RCC predisposition genes (FH, VHL) were detected in 1.4% of the unselected metastatic patients, with higher frequency in non-ccRCC versus ccRCC (6.4% and 0.4%; P = 0.0025) and in younger patients (P = 0.036). Among the 315 studied patients, 14% of non-type 1 papillary cases (4 of 28), all metastatic <1 year after diagnosis, carried a FH germline variant with loss of heterozygosity and tumor genome hypermethylation. Variants in other cancer-associated genes (e.g., MUTYH, BRCA2, CHEK2) occurred in 5.1% of the unselected series, with unclear significance for RCC. CONCLUSION: Our findings confirm a high prevalence of pathogenic germline variants in RCC predisposition genes in metastatic non-ccRCC, and highlight that metastatic patients with papillary type 2 or unconventional histologies compatible with FH would benefit from genetic screening.

Molecular characterization of chromophobe renal cell carcinoma reveals mTOR pathway alterations in patients with poor outcome.

Chromophobe renal cell carcinoma (chRCC) is a histologically and molecularly distinct class of rare renal tumor. TCGA studies revealed low mutational burden, with only TP53 and PTEN recurrently mutated, and discovered alterations in TERT promoter and in the electron transport chain Complex I genes. However, knowledge on drug targetable genes is limited and treatments at metastatic stage do not follow a molecular rationale. In a large series of 92 chRCC enriched with metastatic cases, we performed an in-depth characterization of mTOR pathway alterations through targeted NGS and immunohistochemistry (IHC) of phospho-S6, tuberin, and PTEN. Mutations in mitochondria, telomere maintenance and other renal cancer related genes and p53 IHC, were also assessed. The impact on metastasis development and disease specific survival was determined, using TCGA-KICH series (n = 65) for validation. mTOR pathway mutations (MTOR, TSC1, TSC2) were present in 17% of primary tumors, most of them being classified as pathogenic. Mutations were associated with positive IHC staining of phospho-S6 and PTEN (P = 0.009 and P = 0.001, respectively) and with chRCC eosinophilic variant (P = 0.039), supporting a biological relevance of the pathway. mTOR pathway mutations were associated with worse clinical outcomes. Survival analysis gave a hazard ratio of 5.5 (P = 0.027), and this association was confirmed in TCGA-KICH (HR = 10.3, P = 0.006). TP53 mutations were enriched in metastatic cases (P = 0.018), and mutations in telomere maintenance genes showed a trend in the same direction. p53 IHC staining pattern was associated with the underlying TP53 defect, and negative PTEN IHC staining (82% of cases) suggested PTEN loss as a chRCC hallmark. In conclusion, our study provides with novel genomic knowledge in chRCC and identifies novel markers of poor survival. Furthermore, this is the first study showing that mTOR pathway mutations correlate with poor prognosis, and may help to identify patients with increased sensitivity to mTOR inhibitors.

Advanced sporadic renal epithelioid angiomyolipoma: case report of an extraordinary response to sirolimus linked to TSC2 mutation.

BACKGROUND: Renal epithelioid angiomyolipomas (EAML) are rare tumors with aggressive behavior. EAML can be sporadic or develop within the tuberous sclerosis complex syndrome, where mutations of TSC1 or TSC2 genes (critical negative regulators of mTOR Complex 1) result in an increased activation of mTOR pathway. Optimal EAML treatment, including mTOR inhibitors, remains undetermined. CASE PRESENTATION: Here we present the case of a young adult with a renal EAML that after radical nephrectomy developed metastases, first in liver and then in lumbar vertebrae. After complete surgical resection of these lesions, liver recurrence was detected, this time with incomplete surgical resection. After finding a new liver lesion, systemic treatment with sirolimus started. The patient exhibited a complete and durable response to this drug, being disease free at the time of publication, after 36 months of treatment. Targeted next generation sequencing (NGS) of MTOR, TSC1 and TSC2 genes in the primary tumor, metastasis and blood of the patient, revealed one inactivating TSC2 mutation (c.2739dup; p.K914*) in the tumor cells. Immunohistochemistry revealed decreased TSC2 protein content and increased phospho-S6 in the tumor cells, demonstrating mTOR pathway activation. CONCLUSION: NGS on an EAML patient with an extraordinary response to sirolimus uncovered TSC2 inactivation as the mechanism for the response. This study supports NGS as a useful tool to identify patients sensitive to mTOR inhibitors and supports the treatment of malignant EAML with these drugs.

Biallelic TSC2 Mutations in a Patient With Chromophobe Renal Cell Carcinoma Showing Extraordinary Response to Temsirolimus.

mTOR inhibitors are used to treat renal cell carcinoma (RCC). Treatment response is variable and appears to correlate with genetic alterations that activate mTOR signaling. Recently, everolimus was suggested to be more effective than sunitinib in chromophobe RCC (chRCC), a tumor with frequent mTOR pathway defects. This report presents the genomic and functional characterization of a metastatic chRCC that showed complete response at metastatic sites and 80% reduction in primary tumor size upon temsirolimus treatment. After surgery, the patient remained disease-free for 8 years after temsirolimus therapy. Whole-exome sequencing (WES) revealed 2 somatic variants in TSC2, a critical negative regulator of mTOR: a splicing defect (c.5069-1G>C) and a novel missense variant [c.3200_3201delinsAA; p.(V1067E)]. In vitro functional assessment demonstrated that the V1067E substitution disrupted TSC2 function. Immunohistochemistry in the tumor tissues revealed increased phosphorylated S6 ribosomal protein, indicating mTOR pathway activation. In conclusion, WES revealed TSC2 inactivation as the likely mechanism for this extraordinary response to temsirolimus. These findings support high efficacy of mTOR inhibitors in a subset of patients with chRCC and propose sequencing of mTOR pathway genes to help guide therapy.

Exceptional Response to Temsirolimus in a Metastatic Clear Cell Renal Cell Carcinoma With an Early Novel MTOR-Activating Mutation.

mTOR pathway inhibitors are important drugs for the treatment of advanced renal cell carcinoma (RCC). However, no valid predictive markers have been identified to guide treatment selection and identify patients who are sensitive to these drugs. Mutations activating the mTOR pathway have been suggested to predict response; however, their predictive value is still unclear. Here, we present the genomic and functional characterization of a patient with metastatic clear cell RCC (ccRCC) who experienced a partial response to temsirolimus after a poor response to 2 previous lines of treatment. At the time of publication, the patient was disease-free 8 years after temsirolimus treatment. Multiregion whole-exome sequencing (WES) on 3 regions of the primary tumor, 1 metastasis, and blood revealed tumor mutations in driver genes in ccRCC: a missense mutation in VHL (p.W88L), a loss-of-function mutation in BAP1 (p.E454Rfs*15), and a novel missense mutation in MTOR (p.Y1974H). The MTOR mutation was present in all tumor regions, with similar allele frequency as the VHL mutation, and in vitro functional assessment of the MTOR variant demonstrated that it increased mTORC1 activity. Consistently, immunohistochemistry in the tumor samples demonstrated increased levels of phospho-S6. In conclusion, multiregion WES identified a novel MTOR mutation acquired early during tumor development as the event leading to a high sensitivity to temsirolimus treatment. This study supports tumor multiregion sequencing to detect truncal mutations in the mTOR pathway to identify patients sensitive to mTOR inhibitors.

COVID-19-related temporary disability in healthcare workers in Spain during the four first pandemic waves.

Healthcare workers (HCW) have been the professional category most exposed to SARS-CoV-2. The pandemic's impact on HCW was analyzed in terms of COVID-19-related temporary disability (TD) between February 15th, 2020 and May 1st, 2021. TDs in HCW for COVID-19 infection or quarantine were described. TD quarantine/infection ratios and TDs per 100,000 affiliated HCW were compared with the cumulative incidence (CI) of COVID-19 cases notified to the National Network of Epidemiological Surveillance. TDs rates by economic activity and occupation were computed. A total of 429,127 TDs were recorded, 36,6% for infection. Three-quarters (76%) were women. The median TD quarantine/infection ratio was 2.5 (Interquartile range [IQR] 1.5-3.9). TDs rates in HCW were always above the CI except for the last two months of the fourth wave. Hospital activities accounted for 84% of TDs and showed the highest TD rate for infection (8,279/100,000). Nursing professionals and midwifery, Physicians, and Nursing assistants accounted for 26, 18 and 17 % of the conceded TD respectively, whereas the highest TDs rates were registered among Nursing assistants, Nursing professionals and Physicians: 7,426, 6,925 and 5,508/100,000, respectively. The results indicate the high impact of COVID-19 on HCW in Spain and it's inequalities. They also confirm that TDs represent a complementary source of information for epidemiological and public health surveillance and could provide an early warning of new emerging infections.

Genomic and immune landscape Of metastatic pheochromocytoma and paraganglioma.

The mechanisms triggering metastasis in pheochromocytoma/paraganglioma are unknown, hindering therapeutic options for patients with metastatic tumors (mPPGL). Herein we show by genomic profiling of a large cohort of mPPGLs that high mutational load, microsatellite instability and somatic copy-number alteration burden are associated with ATRX/TERT alterations and are suitable prognostic markers. Transcriptomic analysis defines the signaling networks involved in the acquisition of metastatic competence and establishes a gene signature related to mPPGLs, highlighting CDK1 as an additional mPPGL marker. Immunogenomics accompanied by immunohistochemistry identifies a heterogeneous ecosystem at the tumor microenvironment level, linked to the genomic subtype and tumor behavior. Specifically, we define a general immunosuppressive microenvironment in mPPGLs, the exception being PD-L1 expressing MAML3-related tumors. Our study reveals canonical markers for risk of metastasis, and suggests the usefulness of including immune parameters in clinical management for PPGL prognostication and identification of patients who might benefit from immunotherapy.

[The impact of COVID-19 on sick leave of the persons working in nursing homes in Spain. Usefulness of sick leave for the surveillance of the pandemic evolution.] / El impacto de la Covid-19 en la incapacidad temporal de las personas que trabajan en centros socio-sanitarios en España. Utilidad de la incapacidad temporal para el seguimiento de la evolución de la pandemia.

OBJECTIVE: The nursing homes represented high-risk settings for SARS-CoV-2 infection, both for residents and for the employees. The COVID-19 impact on long-term care facilities (LTCFs) is evaluated, measured through the employees sick leave (SL). The pandemic evolution in the general population aged between 16 and 65 years was analyzed together with the sick leave to assess the latter as a complementary indicator of the SARS-CoV-2 surveillance. METHODS: A descriptive study of all sick leave processes due to COVID-19 recorded between February 15th 2020 and May 1st 2021 in nursing homes was carried out. The close contact sick leave/infection sick leave ratios, the 100,000 affiliated/occupied sick leave rates were computed and compared with the COVID-19 cases cumulative incidence notified to the National Network of epidemiological Surveillance (RENAVE). RESULTS: 261.892 SL processes were recorded. The close contact sick leave/infection sick leave median ratio in nursing homes was 1.8 (Interquartile range, ICR: 1.1-3.3), with values lower than 1 at certain periods. The infection sick leaves were higher in number and ratio and prior to the cases recorded in RENAVE. The sick leave ratio ranged between 81.679/100.000 occupied in nursing homes with medical care and 4.895/100.000 in other residential facilities. CONCLUSIONS: The results confirmed the dramatic impact of COVID-19 in nursing homes and the inequalities characterizing this impact. They also confirmed the potential use of sick leave as an alternative source for epidemiological and public health surveillance, especially now, when the transition of the COVID-19 surveillance to a system not including universal individual surveillance is being discussed.

OBJETIVO: Los centros sociosanitarios representaron entornos de alto riesgo de contagio por SARS-CoV-2, tanto para los residentes como para las personas trabajadoras. Se evaluó el impacto en términos de incapacidad temporal (IT) por COVID-19 en las personas que trabajan en centros sociosanitarios y se comparó con la evolución de la pandemia en la población general de 16 a 65 años, para valorar la utilidad de la IT como indicador complementario de la epidemia por SARS-CoV-2. METODOS: Se realizó un estudio descriptivo de todos los procesos de incapacidad temporal por COVID-19 registrados entre el 15 de febrero de 2020 y el 1 de mayo de 2021 en establecimientos residenciales. Se obtuvieron las ratios de incapacidad temporal por contacto estrecho /incapacidad temporal por infección, las tasas de incapacidad temporal por 100.000 afiliados/ocupados y se compararon con la incidencia acumulada de casos COVID-19 notificados a la Red Nacional de Vigilancia Epidemiológica (RENAVE). RESULTADOS: Se registraron 261.892 procesos de incapacidad temporal. La mediana de la ratio de incapacidad temporal por contacto estrecho /incapacidad temporal por infección en residencias fue de 1,8 (Rango intercuartílico, RIC: 1,1-3,3), con valores menores a 1 en periodos. Las IT por infección fueron superiores en número, tasa y anteriores en el tiempo a los casos registrados en RENAVE. Por tipo de residencia, la tasa de incapacidad temporal osciló entre 81.679/100.000 ocupados en asistencia en establecimientos residenciales con cuidados sanitaros y 4.895/100.000 en otros establecimientos residenciales. CONCLUSIONES: Los resultados confirmaron el enorme impacto que tuvo la COVID-19 en los centros sociosanitarios y la desigualdad que ha caracterizado este impacto. Apoyan también la posible utilización de la incapacidad temporal como fuente de información alternativa para la vigilancia epidemiológica y de salud pública, lo cual resulta de especial interés en este momento en el que se está planteando una transición en la vigilancia del COVID-19 hacia un sistema que ya no incluya una vigilancia individualizada universal.

[Contribution of the occupational health to the COVID-19 pandemic control.] / Contribución de la salud laboral al control de la pandemia por covid-19 en España.

When the World Health Organization declared Covid-19 as a public health emergency of international concern, the Spanish Ministry of Health called the health, labor, social security authorities, Labor and Social Security Inspection, National Institute of Security and Occupational Health, employers, unions, occupational risk prevention services, mutual societies and scientific societies of occupational medicine and nursing, to collaborate in the control of the transmission of SARS-CoV-2 in companies. The Occupational Health Group of the Public Health Commission of the Interterritorial Council of the National Health System, developed the Procedure for the prevention of occupational risks in the face of exposure to SARS-CoV-2, which has been updated 15 times until the date. It contains the prevention measures to be implemented in the workplaces: organizational and collective protection, personal protection, especially vulnerable worker and risk level, study and management of cases and contacts that occurred in the company, collaboration in the management of temporary disability and, more recently, reincorporation and management of vaccinated workers. As a result of these cooperation and collaboration frameworks, a series of activities were deployed in the workplace, which are described in this article.

Cuando la Organización Mundial de la Salud declaró la Covid-19 como una emergencia de salud pública de importancia internacional, el Ministerio de Sanidad convocó a las autoridades sanitarias, laborales, de seguridad social, Inspección de Trabajo y Seguridad Social, Instituto Nacional de Seguridad y Salud en el Trabajo, empresarios, sindicatos, servicios de prevención de riesgos laborales, mutuas y sociedades científicas de la medicina y enfermería del trabajo, para colaborar en el control de la transmisión del SARS-CoV-2 en el ámbito de las empresas. La Ponencia de Salud Laboral de la Comisión de Salud Pública del Consejo Interterritorial del Sistema Nacional de Salud, elaboró el Procedimiento para los servicios de prevención de riesgos laborales frente a la exposición al SARS-CoV-2, que se ha actualizado 15 veces hasta la fecha. En él se recogen las medidas de prevención a implantar en los centros de trabajo: de carácter organizativo y de protección colectiva, de protección personal, de trabajador especialmente vulnerable y nivel de riesgo, de estudio y manejo de casos y contactos ocurridos en la empresa, de colaboración en la gestión de la incapacidad temporal y, más recientemente, de reincorporación y gestión de las y los trabajadores vacunados. Como resultado de esos marcos de cooperación y colaboración se desplegaron una serie de actividades en los lugares de trabajo que son descritas en este artículo.

A Novel Approach for the Identification of Pharmacogenetic Variants in MT-RNR1 through Next-Generation Sequencing Off-Target Data.

Specific genetic variants in the mitochondrially encoded 12S ribosomal RNA gene (MT-RNR1) cause aminoglycoside-induced irreversible hearing loss. Mitochondrial DNA is usually not included in targeted sequencing experiments; however, off-target data may deliver this information. Here, we extract MT-RNR1 genetic variation, including the most relevant ototoxicity variant m.1555A>G, using the off-target reads of 473 research samples, sequenced through a capture-based, custom-targeted panel and whole exome sequencing (WES), and of 1245 diagnostic samples with clinical WES. Sanger sequencing and fluorescence-based genotyping were used for genotype validation. There was a correlation between off-target reads and mitochondrial coverage (rcustomPanel = 0.39, p = 2 × 10-13 and rWES = 0.67, p = 7 × 10-21). The median read depth of MT-RNR1 m.1555 was similar to the average mitochondrial genome coverage, with saliva and blood samples giving comparable results. The genotypes from 415 samples, including three m.1555G carriers, were concordant with fluorescence-based genotyping data. In clinical WES, median MT-RNR1 coverage was 56×, with 90% of samples having ≥20 reads at m.1555 position, and one m.1494T and three m.1555G carriers were identified with no evidence for heteroplasmy. Altogether, this study shows that obtaining MT-RNR1 genotypes through off-target reads is an efficient strategy that can impulse preemptive pharmacogenetic screening of this mitochondrial gene.

CD133 Expression in Medullary Thyroid Cancer Cells Identifies Patients with Poor Prognosis.

CONTEXT: The identification of markers able to determine medullary thyroid cancer (MTC) patients at high-risk of disease progression is critical to improve their clinical management and outcome. Previous studies have suggested that expression of the stem cell marker CD133 is associated with MTC aggressiveness. OBJECTIVE: To evaluate CD133 impact on disease progression in MTC and explore the regulatory mechanisms leading to the upregulation of this protein in aggressive tumors. PATIENTS: We compiled a series of 74 MTCs with associated clinical data and characterized them for mutations in RET and RAS proto-oncogenes, presumed to be related with disease clinical behavior. RESULTS: We found that CD133 immunohistochemical expression was associated with adverse clinicopathological features and predicted a reduction in time to disease progression even when only RET-mutated cases were considered in the analysis (log-rank test P < 0.003). Univariate analysis for progression-free survival revealed CD133 expression and presence of tumor emboli in peritumoral blood vessels as the most significant prognostic covariates among others such as age, gender, and prognostic stage. Multivariate analysis identified both variables as independent factors of poor prognosis (hazard ratio = 16.6 and 2; P = 0.001 and 0.010, respectively). Finally, we defined hsa-miR-30a-5p, a miRNA downregulated in aggressive MTCs, as a CD133 expression regulator. Ectopic expression of hsa-miR-30a-5p in MZ-CRC-1 (RETM918T) cells significantly reduced CD133 mRNA expression. CONCLUSIONS: Our results suggest that CD133 expression may be a useful tool to identify MTC patients with poor prognosis, who may benefit from a more extensive primary surgical management and follow-up.

Prognostic and Predictive Value of PBRM1 in Clear Cell Renal Cell Carcinoma.

Renal cell carcinoma (RCC) is the most frequent kidney solid tumor, the clear cell RCC (ccRCC) being the major histological subtype. The probability of recurrence and the clinical behavior of ccRCC will greatly depend on the different clinical and histopathological features, already incorporated to different scoring systems, and on the genomic landscape of the tumor. In this sense, ccRCC has for a long time been known to be associated to the biallelic inactivation of Von Hippel-Lindau (VHL) gene which causes aberrant hypoxia inducible factor (HIF) accumulation. Recently, next generation-sequencing technologies have provided the bases for an in-depth molecular characterization of ccRCC, identifying additional recurrently mutated genes, such as PBRM1 (≈40-50%), SETD2 (≈12%), or BAP1 (≈10%). PBRM1, the second most common mutated gene in ccRCC after VHL, is a component of the SWI/SNF chromatin remodeling complex. Different studies have investigated the biological consequences and the potential role of PBRM1 alterations in RCC prognosis and as a drug response modulator, although some results are contradictory. In the present article, we review the current evidence on PBRM1 as potential prognostic and predictive marker in both localized and metastatic RCC.

Integrative multi-omics analysis identifies a prognostic miRNA signature and a targetable miR-21-3p/TSC2/mTOR axis in metastatic pheochromocytoma/paraganglioma.

Rationale: Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors that present variable outcomes. To date, no effective therapies or reliable prognostic markers are available for patients who develop metastatic PPGL (mPPGL). Our aim was to discover robust prognostic markers validated through in vitro models, and define specific therapeutic options according to tumor genomic features. Methods: We analyzed three PPGL miRNome datasets (n=443), validated candidate markers and assessed them in serum samples (n=36) to find a metastatic miRNA signature. An integrative study of miRNome, transcriptome and proteome was performed to find miRNA targets, which were further characterized in vitro. Results: A signature of six miRNAs (miR-21-3p, miR-183-5p, miR-182-5p, miR-96-5p, miR-551b-3p, and miR-202-5p) was associated with metastatic risk and time to progression. A higher expression of five of these miRNAs was also detected in PPGL patients' liquid biopsies compared with controls. The combined expression of miR-21-3p/miR-183-5p showed the best power to predict metastasis (AUC=0.804, P=4.67·10-18), and was found associated in vitro with pro-metastatic features, such as neuroendocrine-mesenchymal transition phenotype, and increased cell migration rate. A pan-cancer multi-omic integrative study correlated miR-21-3p levels with TSC2 expression, mTOR pathway activation, and a predictive signature for mTOR inhibitor-sensitivity in PPGLs and other cancers. Likewise, we demonstrated in vitro a TSC2 repression and an enhanced rapamycin sensitivity upon miR-21-3p expression. Conclusions: Our findings support the assessment of miR-21-3p/miR-183-5p, in tumors and liquid biopsies, as biomarkers for risk stratification to improve the PPGL patients' management. We propose miR-21-3p to select mPPGL patients who may benefit from mTOR inhibitors.