Implications of noncoding regulatory functions in the development of insulinomas.

Insulinomas are rare neuroendocrine tumors arising from pancreatic ß cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in ß cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of ß cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations.

Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis.

Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of hematologic malignancies, cardiovascular diseases, and other conditions. Although the most frequently mutated CH driver genes have been identified, a systematic landscape of the mutations capable of initiating this phenomenon is still lacking. Here, we trained machine-learning models for 12 of the most recurrent CH genes to identify their driver mutations. These models outperform expert-curated rules based on prior knowledge of the function of these genes. Moreover, their application to identify CH driver mutations across almost half a million donors of the UK Biobank reproduces known associations between CH driver mutations and age, and the prevalence of several diseases and conditions. We thus propose that these models support the accurate identification of CH across healthy individuals.

Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma.

Resistance to MAPK inhibitors (MAPKi), the main cause of relapse in BRAF-mutant melanoma, is associated with the production of alternative BRAF mRNA isoforms (altBRAFs) in up to 30% of patients receiving BRAF inhibitor monotherapy. These altBRAFs have been described as being generated by alternative pre-mRNA splicing, and splicing modulation has been proposed as a therapeutic strategy to overcome resistance. In contrast, we report that altBRAFs are generated through genomic deletions. Using different in vitro models of altBRAF-mediated melanoma resistance, we demonstrate the production of altBRAFs exclusively from the BRAF V600E allele, correlating with corresponding genomic deletions. Genomic deletions are also detected in tumor samples from melanoma and breast cancer patients expressing altBRAFs. Along with the identification of altBRAFs in BRAF wild-type and in MAPKi-naive melanoma samples, our results represent a major shift in our understanding of mechanisms leading to the generation of BRAF transcripts variants associated with resistance in melanoma.

Origins of Second Malignancies in Children and Mutational Footprint of Chemotherapy in Normal Tissues.

Pediatric cancers are rare diseases, and children without known germline predisposing conditions who develop a second malignancy during developmental ages are extremely rare. We present four such clinical cases and, through whole-genome and error-correcting ultra-deep duplex sequencing of tumor and normal samples, we explored the origin of the second malignancy in four children, uncovering different routes of development. The exposure to cytotoxic therapies was linked to the emergence of a secondary acute myeloid leukemia. A common somatic mutation acquired early during embryonic development was the driver of two solid malignancies in another child. In two cases, the two tumors developed from completely independent clones diverging during embryogenesis. Importantly, we demonstrate that platinum-based therapies contributed at least one order of magnitude more mutations per day of exposure than aging to normal tissues in these children. SIGNIFICANCE: Using whole-genome and error-correcting ultra-deep duplex sequencing, we uncover different origins for second neoplasms in four children. We also uncover the presence of platinum-related mutations across 10 normal tissues of exposed individuals, highlighting the impact that the use of cytotoxic therapies may have on cancer survivors. See related commentary by Pacyna and Nangalia, p. 900. This article is featured in Selected Articles from This Issue, p. 897.

Hotspot propensity across mutational processes.

The sparsity of mutations observed across tumours hinders our ability to study mutation rate variability at nucleotide resolution. To circumvent this, here we investigated the propensity of mutational processes to form mutational hotspots as a readout of their mutation rate variability at single base resolution. Mutational signatures 1 and 17 have the highest hotspot propensity (5-78 times higher than other processes). After accounting for trinucleotide mutational probabilities, sequence composition and mutational heterogeneity at 10 Kbp, most (94-95%) signature 17 hotspots remain unexplained, suggesting a significant role of local genomic features. For signature 1, the inclusion of genome-wide distribution of methylated CpG sites into models can explain most (80-100%) of the hotspot propensity. There is an increased hotspot propensity of signature 1 in normal tissues and de novo germline mutations. We demonstrate that hotspot propensity is a useful readout to assess the accuracy of mutation rate models at nucleotide resolution. This new approach and the findings derived from it open up new avenues for a range of somatic and germline studies investigating and modelling mutagenesis.

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that-in the case of the interdependent tumor cell morphology and adapted immune response-reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.

Copy number footprints of platinum-based anticancer therapies.

Recently, distinct mutational footprints observed in metastatic tumors, secondary malignancies and normal human tissues have been demonstrated to be caused by the exposure to several chemotherapeutic drugs. These characteristic mutations originate from specific lesions caused by these chemicals to the DNA of exposed cells. However, it is unknown whether the exposure to these chemotherapies leads to a specific footprint of larger chromosomal aberrations. Here, we address this question exploiting whole genome sequencing data of metastatic tumors obtained from patients exposed to different chemotherapeutic drugs. As a result, we discovered a specific copy number footprint across tumors from patients previously exposed to platinum-based therapies. This footprint is characterized by a significant increase in the number of chromosomal fragments of copy number 1-4 and size smaller than 10 Mb in exposed tumors with respect to their unexposed counterparts (median 14-387% greater across tumor types). The number of chromosomal fragments characteristic of the platinum-associated CN footprint increases significantly with the activity of the well known platinum-related footprint of single nucleotide variants across exposed tumors.

Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis.

Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of a number of hematologic malignancies, cardiovascular diseases and other conditions. Although the most frequently mutated CH driver genes have been identified, a systematic landscape of the mutations capable of initiating this phenomenon is still lacking. Here, we train high-quality machine-learning models for 12 of the most recurrent CH driver genes to identify their driver mutations. These models outperform an experimental base-editing approach and expert-curated rules based on prior knowledge of the function of these genes. Moreover, their application to identify CH driver mutations across almost half a million donors of the UK Biobank reproduces known associations between CH driver mutations and age, and the prevalence of several diseases and conditions. We thus propose that these models support the accurate identification of CH across healthy individuals.

Hypopigmentation in mantled howler monkeys Alouatta palliata (gray 1849): First documented cases of whole-body leucism in South America.

The existence of hypopigmentation like leucism is the result of genetic anomalies that might be enhanced by external factors such as pollution. This anomaly may reduce survival rates. Leucism has been recorded in wildlife, but overall, it is considered very rare. There have been few records of mantled howler monkeys with leucism in Mexico and Costa Rica, but whole-body leucism in howler monkeys from South America was unknown. In this article, we report for the first-time documented cases of whole-body leucism in young individuals of mantled howler monkeys Alouatta palliata in an isolated remanent of tropical dry forest in southwestern Ecuador known as Cerro Blanco Protective Forest. In total, we found two juvenile individuals with leucism in October 2021. The report of howler monkeys with whole-body leucism may be caused by two processes: inbreeding because of isolated populations, environmental pressure caused by pollution, or the interaction of both. Our findings also reveal that hypopigmentation is becoming more frequent in howler monkey populations along its distributional range. Therefore, it is important to promote research in this field to disentangle the causes of hypopigmentation and to consider a regional management strategy for the species.

La existencia de afecciones que causan hipopigmentación, como el leucismo, son el resultado de anomalías genéticas que pueden verse potenciadas por factores externos como la contaminación. Estas anomalías puedes reducir las tasas de supervivencia. Se ha registrado leucismo en la vida silvestre, pero en general, se considera muy raro. En México y Costa Rica se ha reportado la existencia de casos aislados de monos aulladores de manto con leucismo, pero se desconocía el leucismo de cuerpo completo en monos aulladores para América del Sur. En este artículo, reportamos por primera vez casos documentados de leucismo en todo el cuerpo en individuos juveniles de monos aulladores de manto Alouatta palliata en un remanente aislado de bosque seco tropical en el suroeste de Ecuador conocido como Bosque Protector Cerro Blanco. En total, encontramos dos individuos juveniles con leucismo en octubre de 2021. Este reporte de monos aulladores con leucismo en todo el cuerpo puede ser causado por dos procesos: apareamiento dentro de individuos de la misma población causado por el aislamiento, la presión ambiental causada por la contaminación o la interacción de ambos. Nuestros hallazgos también revelan que la hipopigmentación es cada vez más frecuente en las poblaciones de monos aulladores a lo largo de su rango de distribución. Por lo tanto, es importante promover la investigación en este campo para determinar las causas de la hipopigmentación y considerar una estrategia de manejo regional para la especie. Palabras clave: aberraciones cromáticas, pérdida de conectividad, anomalías genéticas, endogamia, cambio de pigmentación en primates por contaminación, Bosque Seco del Pacífico Ecuatorial.

New insights into the structural transition from UO2+x to U3O7 by quantitative Raman spectroscopy.

The study of uranium oxides at different conditions is of paramount importance in the nuclear field, especially regarding characterization of the spent nuclear fuel behavior in dry storage scenarios. This paper reports results of XRD and Raman analysis on four powdered samples prepared in order to cover a specific stoichiometry range in UO2+x, i.e. x = 0.24, 0.26, 0.28 and 0.30. XRD results reveal a clear increase of the average tetragonal distortion with the increase in oxidation degree, with the main phase detected for all the samples being a weakly tetragonal phase identified as U3O7-z (c/a ≪ 1.032). U4O9 has not been detected in any sample. The Raman study carried out consists of both qualitative and quantitative analysis. The former, where a profile analysis has been performed on the acquired spectra, shows that the most intense bands (centered at ∼455 and ∼635 cm-1) are actually a doublet each, in agreement with a previous experimental study. Moreover, this work shows, for the first time, that the band at ∼160 cm-1 is also a doublet, which makes its classical assignment no longer obvious. The most important and original results from this study are obtained by applying Quantitative Raman Spectroscopy (QRS). This analysis shows that the second contribution at ∼475 cm-1 to the known T2g mode increases its relative intensity with the oxidation degree. This contribution may be related to the tetragonal distortion occurring in the cubic UO2 lattice due to the addition of interstitial oxygen, based on its comparison with the obtained XRD outcomes. In addition, the so-called "defects band" (centered at around 600 cm-1) presents a remarkable kink, of around 20 cm-1, in its Raman shift between UO2.26 and UO2.28. Such behavior might be directly associated with the observed appearance of the stoichiometric U3O7 phase (c/a = 1.032) for UO2.28 and UO2.30.

High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer.

CDK4/6 inhibitors combined with endocrine therapy have demonstrated higher antitumor activity than endocrine therapy alone for the treatment of advanced estrogen receptor-positive breast cancer. Some of these tumors are de novo resistant to CDK4/6 inhibitors and others develop acquired resistance. Here, we show that p16 overexpression is associated with reduced antitumor activity of CDK4/6 inhibitors in patient-derived xenografts (n = 37) and estrogen receptor-positive breast cancer cell lines, as well as reduced response of early and advanced breast cancer patients to CDK4/6 inhibitors (n = 89). We also identified heterozygous RB1 loss as biomarker of acquired resistance and poor clinical outcome. Combination of the CDK4/6 inhibitor ribociclib with the PI3K inhibitor alpelisib showed antitumor activity in estrogen receptor-positive non-basal-like breast cancer patient-derived xenografts, independently of PIK3CA, ESR1 or RB1 mutation, also in drug de-escalation experiments or omitting endocrine therapy. Our results offer insights into predicting primary/acquired resistance to CDK4/6 inhibitors and post-progression therapeutic strategies.

Discovering the drivers of clonal hematopoiesis.

Mutations in genes that confer a selective advantage to hematopoietic stem cells (HSCs) drive clonal hematopoiesis (CH). While some CH drivers have been identified, the compendium of all genes able to drive CH upon mutations in HSCs remains incomplete. Exploiting signals of positive selection in blood somatic mutations may be an effective way to identify CH driver genes, analogously to cancer. Using the tumor sample in blood/tumor pairs as reference, we identify blood somatic mutations across more than 12,000 donors from two large cancer genomics cohorts. The application of IntOGen, a driver discovery pipeline, to both cohorts, and more than 24,000 targeted sequenced samples yields a list of close to 70 genes with signals of positive selection in CH, available at http://www.intogen.org/ch . This approach recovers known CH genes, and discovers other candidates.

First description of sarcoptic mange in a wild coati (Nasua narica), in Ecuador, and cooccurrence of canine distemper virus.

We present a case of Sarcoptes and canine distemper virus (CDV) infection in a white-nosed coati (Nasua narica) that was trapped in the dry tropical forest of Cerro Blanco reserve, located in the coastal region of Ecuador. Sarcoptic mange is a highly contagious and zoonotic disease with worldwide distribution that causes epidemics. Mange is produced by Sarcoptes mites that causes severe epidermal damage. Secondary infections and physiological constrictions without treatment can lead to death of the host. In addition, cooccurrence of canine distemper virus was detected via iiRT-PCR from serum samples. Physical analyses showed that 90% of the skin was affected by severe alopecia due to the sarcoptic mange infection. The presence of mites and histopathological analyses confirmed the diagnosis of infection. This coati was taken to a veterinary clinic and was fed every day, but it died after four days. This is the first report of sarcoptic mange and the first report of CDV in white-nosed coatis in South America. Further studies are needed in this region, to seek out other suspected cases, given the high capacity for disease transmission. Preventive actions to avoid epidemic and zoonotic episodes are needed.

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.

MOTIVATION: DNA methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods use either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination. RESULTS: Here, we present DeepMP, a convolutional neural network-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on Escherichia coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets. AVAILABILITY AND IMPLEMENTATION: DeepMP is implemented and freely available under MIT license at https://github.com/pepebonet/DeepMP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

First description of sarcoptic mange in a wild coati (Nasua narica), in Ecuador, and cooccurrence of canine distemper virus / Primeira descrição da sarna sarcóptica em um coati selvagem (Nasua narica), no Equador, e coocorrência do vírus distemper canino

Abstract We present a case of Sarcoptes and canine distemper virus (CDV) infection in a white-nosed coati (Nasua narica) that was trapped in the dry tropical forest of Cerro Blanco reserve, located in the coastal region of Ecuador. Sarcoptic mange is a highly contagious and zoonotic disease with worldwide distribution that causes epidemics. Mange is produced by Sarcoptes mites that causes severe epidermal damage. Secondary infections and physiological constrictions without treatment can lead to death of the host. In addition, cooccurrence of canine distemper virus was detected via iiRT-PCR from serum samples. Physical analyses showed that 90% of the skin was affected by severe alopecia due to the sarcoptic mange infection. The presence of mites and histopathological analyses confirmed the diagnosis of infection. This coati was taken to a veterinary clinic and was fed every day, but it died after four days. This is the first report of sarcoptic mange and the first report of CDV in white-nosed coatis in South America. Further studies are needed in this region, to seek out other suspected cases, given the high capacity for disease transmission. Preventive actions to avoid epidemic and zoonotic episodes are needed.

Resumo Apresentamos um caso de Sarcoptes e infecção pelo vírus da cinomose canina (CDV) em um quati-do-nariz-branco (Nasua narica) que ficou preso na floresta tropical seca da reserva de Cerro Blanco, localizada na região costeira do Equador. A sarna sarcóptica é uma doença altamente contagiosa e zoonótica de distribuição mundial que causa epidemias. A sarna é produzida por ácaro do gênero Sarcoptes que causa graves danos epidérmicos. Infecções secundárias e constrições fisiológicas sem tratamento podem levar à morte do organismo. Além disso, a coocorrência do vírus da cinomose canina foi detectada, via iiRT-PCR, a partir de amostras de soro. As análises físicas mostraram que 90% da pele estava afetada por alopecia severa devido à infecção pelo ácaro da sarna sarcóptica. A presença de ácaros e análises histopatológicas confirmaram o diagnóstico de infecção. Esse quati foi levado a uma clínica veterinária e foi alimentado todos os dias, mas morreu após quatro dias. Esse é o primeiro relato de sarna sarcóptica e o primeiro relato de CDV em quatis-de-nariz-branco na América do Sul. São necessários mais estudos nessa região, para buscar outros casos suspeitos, dada a alta capacidade de transmissão da doença. Ações preventivas para evitar episódios epidêmicos e zoonóticos, são necessárias.

Genomic and evolutionary classification of lung cancer in never smokers.

Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined by copy number aberrations. The dominant subtype (piano), which is rare in lung cancer in smokers, features somatic UBA1 mutations, germline AR variants and stem cell-like properties, including low mutational burden, high intratumor heterogeneity, long telomeres, frequent KRAS mutations and slow growth, as suggested by the occurrence of cancer drivers' progenitor cells many years before tumor diagnosis. The other subtypes are characterized by specific amplifications and EGFR mutations (mezzo-forte) and whole-genome doubling (forte). No strong tobacco smoking signatures were detected, even in cases with exposure to secondhand tobacco smoke. Genes within the receptor tyrosine kinase-Ras pathway had distinct impacts on survival; five genomic alterations independently doubled mortality. These findings create avenues for personalized treatment in LCINS.

The evolution of hematopoietic cells under cancer therapy.

Chemotherapies may increase mutagenesis of healthy cells and change the selective pressures in tissues, thus influencing their evolution. However, their contributions to the mutation burden and clonal expansions of healthy somatic tissues are not clear. Here, exploiting the mutational footprint of some chemotherapies, we explore their influence on the evolution of hematopoietic cells. Cells of Acute Myeloid Leukemia (AML) secondary to treatment with platinum-based drugs show the mutational footprint of these drugs, indicating that non-malignant blood cells receive chemotherapy mutations. No trace of the 5-fluorouracil (5FU) mutational signature is found in AMLs secondary to exposure to 5FU, suggesting that cells establishing the leukemia could be quiescent during treatment. Using the platinum-based mutational signature as a barcode, we determine that the clonal expansion originating the secondary AMLs begins after the start of the cytotoxic treatment. Its absence in clonal hematopoiesis cases is consistent with the start of the clonal expansion predating the exposure to platinum-based drugs.