Multistep tumor genetic evolution and changes in immunogenicity trigger immune-mediated disease eradication in stage IV melanoma: lessons from a single case

Durable remissions are observed in 10%-20% of treated patients with advanced metastatic melanoma but the factors associated with long-term complete clinical responses are largely unknown. Here, we report the molecular characteristics of tumor evolution during disease progression along a 9-year clinical course in a patient with advanced disseminated melanoma who received different treatments, including trametinib, ipilimumab, radiation, vemurafenib, surgical tumor debulking and a second ipilimumab course, ultimately achieving complete long-term disease remission.Longitudinal analyses of therapies-resistant metastatic tumors revealed the effects of different treatments on tumor's microenvironment and immunogenicity, ultimately creating a milieu favorable to immunotherapy response. Monitoring of the temporal dynamics of T cells by analysis of the T cell receptor (TCR) repertoire in the tumor and peripheral blood during disease evolution indicated that T-cell clones with common TCR rearrangements, present at low levels at baseline, were maintained and expanded after immunotherapy, and that TCR diversity increased. Analysis of genetic, molecular, and cellular components of the tumor depicted a multistep process in which treatment with kinase inhibitors strongly conditioned the immune microenvironment creating an inflamed milieu converting cold into hot tumors, while ipilimumab impacted and increased the TCR repertoire, a requirement for tumor rejection.Since the optimal sequencing of treatment with antibodies targeting immune checkpoints and kinase inhibitors for advanced melanoma is still clinically debated, this case indicates that immunotherapy success is possible even after progression on targeted therapy.

Genomic and transcriptomic analyses of thyroid cancers identify DICER1 somatic mutations in adult follicular-patterned RAS-like tumors

Background

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Several genomic and transcriptomic studies explored the molecular landscape of follicular cell-derived TCs, and BRAFV600E, RAS mutations, and gene fusions are well-established drivers. DICER1 mutations were described in specific sets of TC patients but represent a rare event in adult TC patients.

Methods

Here, we report the molecular characterization of 30 retrospective follicular cell-derived thyroid tumors, comprising PTCs (90%) and poorly differentiated TCs (10%), collected at our Institute. We performed DNA whole-exome sequencing using patient-matched control for somatic mutation calling, and targeted RNA-seq for gene fusion detection. Transcriptional profiles established in the same cohort by microarray were investigated using three signaling-related gene signatures derived from The Cancer Genome Atlas (TCGA).

Results

The occurrence of BRAFV600E (44%), RAS mutations (13%), and gene fusions (13%) was confirmed in our cohort. In addition, in two patients lacking known drivers, mutations of the DICER1 gene (p.D1709N and p.D1810V) were identified. DICER1 mutations occur in two adult patients with follicular-pattern lesions, and in one of them a second concurrent DICER1 mutation (p.R459*) is also observed. Additional putative drivers include ROS1 gene (p.P2130A mutation), identified in a patient with a rare solid-trabecular subtype of PTC. Transcriptomics indicates that DICER1 tumors are RAS-like, whereas the ROS1-mutated tumor displays a borderline RAS-/BRAF-like subtype. We also provide an overview of DICER1 and ROS1 mutations in thyroid lesions by investigating the COSMIC database.

Conclusion

Even though small, our series recapitulates the genetic background of PTC. Furthermore, we identified DICER1 mutations, one of which is previously unreported in thyroid lesions. For these less common alterations and for patients with unknown drivers, we provide signaling information applying TCGA-derived classification.

Bitter Is Better: Wild Greens Used in the Blue Zone of Ikaria, Greece

The current study reports an ethnobotanical field investigation of traditionally gathered and consumed wild greens (Chorta) in one of the five so-called Blue Zones in the world: Ikaria Isle, Greece. Through 31 semi-structured interviews, a total of 56 wild green plants were documented along with their culinary uses, linguistic labels, and locally perceived tastes. Most of the gathered greens were described as bitter and associated with members of Asteraceae and Brassicaceae botanical families (31%), while among the top-quoted wild greens, species belonging to these two plant families accounted for 50% of the wild vegetables, which were consumed mostly cooked. Cross-cultural comparison with foraging in other areas of the central-eastern Mediterranean and the Near East demonstrated a remarkable overlapping of Ikarian greens with Cretan and Sicilian, as well as in the prevalence of bitter-tasting botanical genera. Important differences with other wild greens-related food heritage were found, most notably with the Armenian and Kurdish ones, which do not commonly feature many bitter greens. The proven role of extra-oral bitter taste receptors in the modulation of gastric emptying, glucose absorption and crosstalk with microbiota opens new ways of looking at these differences, in particular with regard to possible health implications. The present study is also an important attempt to preserve and document the bio-cultural gastronomic heritage of Chorta as a quintessential part of the Mediterranean diet. The study recommends that nutritionists, food scientists, and historians, as well as policymakers and practitioners, pay the required attention to traditional rural dietary systems as models of sustainable health.

Molecular Tumor Board as a Clinical Tool for Converting Molecular Data Into Real-World Patient Care

PURPOSE

The investigation of multiple molecular targets with next-generation sequencing (NGS) has entered clinical practice in oncology, yielding to a paradigm shift from the histology-centric approach to the mutational model for personalized treatment. Accordingly, most of the drugs recently approved in oncology are coupled to specific biomarkers. One potential tool for implementing the mutational model of precision oncology in daily practice is represented by the Molecular Tumor Board (MTB), a multidisciplinary team whereby molecular pathologists, biologists, bioinformaticians, geneticists, medical oncologists, and pharmacists cooperate to generate, interpret, and match molecular data with personalized treatments.

PATIENTS AND METHODS

Since May 2020, the institutional MTB set at Fondazione IRCCS Istituto Nazionale Tumori of Milan met weekly via teleconference to discuss molecular data and potential therapeutic options for patients with advanced/metastatic solid tumors.

RESULTS

Up to October 2021, among 1,996 patients evaluated, we identified >10,000 variants, 43.2% of which were functionally relevant (pathogenic or likely pathogenic). On the basis of functionally relevant variants, 711 patients (35.6%) were potentially eligible to targeted therapy according to European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets tiers, and 9.4% received a personalized treatment. Overall, larger NGS panels (containing >50 genes) significantly outperformed small panels (up to 50 genes) in detecting actionable gene targets across different tumor types.

CONCLUSION

Our real-world data provide evidence that MTB is a valuable tool for matching NGS data with targeted treatments, eventually implementing precision oncology in clinical practice.

Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples

Aim:

Diagnostic laboratories are progressively introducing next-generation sequencing (NGS) technologies in the routine workflow to meet the increasing clinical need for comprehensive molecular characterization in cancer patients for diagnosis and precision medicine, including fusion-transcripts detection. Nevertheless, the low quality of messenger RNA (mRNA) extracted from formalin-fixed paraffin-embedded (FFPE) samples may affect the transition from traditional single-gene testing approaches [like fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or polymerase chain reaction (PCR)] to NGS. The present study is aimed at assessing the overall accuracy of RNA fusion transcripts detection by NGS analysis in FFPE samples in real-world diagnostics.

Methods:

Herein, NGS data from 190 soft tissue tumors (STTs) and carcinoma cases, discussed in the context of the institutional Molecular Tumor Board, are reported and analyzed by FusionPlex^© Solid tumor kit through the manufacturer’s pipeline and by two well-known fast and accurate open-source tools [Arriba (ARR) and spliced transcripts alignment to reference (STAR)-fusion (SFU)].

Results:

The combination of FusionPlex^© Solid tumor with ArcherDX^® Analysis suite (ADx) analysis package has been proven to be sensitive and specific in STT samples, while partial loss of sensitivity has been found in carcinoma specimens.

Conclusions:

Albeit ARR and SFU showed lower sensitivity, the use of additional fusion-detection tools can contribute to reinforcing or extending the output obtained by ADx, particularly in the case of low-quality input data. Overall, our results sustain the clinical use of NGS for the detection of fusion transcripts in FFPE material.

Genetic Variants and Somatic Alterations Associated with MITF-E318K Germline Mutation in Melanoma Patients

The MITF-E318K variant has been implicated in genetic predisposition to cutaneous melanoma. We addressed the occurrence of MITF-E318K and its association with germline status of CDKN2A and MC1R genes in a hospital-based series of 248 melanoma patients including cohorts of multiple, familial, pediatric, sporadic and melanoma associated with other tumors. Seven MITF-E318K carriers were identified, spanning every group except the pediatric patients. Three carriers showed mutated CDKN2A, five displayed MC1R variants, while the sporadic carrier revealed no variants. Germline/tumor whole exome sequencing for this carrier revealed germline variants of unknown significance in ATM and FANCI genes and, in four BRAF-V600E metastases, somatic loss of the MITF wild-type allele, amplification of MITF-E318K and deletion of a 9p21.3 chromosomal region including CDKN2A and MTAP. In silico analysis of tumors from MITF-E318K melanoma carriers in the TCGA Pan-Cancer-Atlas dataset confirmed the association with BRAF mutation and 9p21.3 deletion revealing a common genetic pattern. MTAP was the gene deleted at homozygous level in the highest number of patients. These results support the utility of both germline and tumor genome analysis to define tumor groups providing enhanced information for clinical strategies and highlight the importance of melanoma prevention programs for MITF-E318K patients.

Pre-operative micronutrient deficiencies in patients with severe obesity candidates for bariatric surgery

PURPOSE

In patients with obesity, micronutrient deficiencies have been reported both before and after bariatric surgery (BS). Obesity is a chronic pro-inflammatory status, and inflammation increases the risk of micronutrient malnutrition. Our objective was to assess in pre-BS patients the prevalence of micronutrient deficiencies and their correlation with blood values of C-reactive protein (CRP).

METHODS

Anthropometric data, instrumental examinations, and blood variables were centrally measured in the first 200 patients undergoing a pre-BS evaluation at the "Città della Salute e della Scienza" Hospital of Torino, starting from January 2018.

RESULTS

At least one micronutrient deficiency was present in 85.5% of pre-BS patients. Vitamin D deficiency was the most prevalent (74.5%), followed by folate (33.5%), iron (32%), calcium (13%), vitamin B12 (10%), and albumin (5.5%) deficiency. CRP values were high (> 5 mg/L) in 65% of the patients. These individuals showed increased rate of iron, folate, vitamin B12 deficiency, and a higher number of micronutrient deficiencies. In a multiple logistic regression model, increased CRP levels were significantly associated with deficiencies of vitamin B12 (OR = 5.84; 95% CI 1.25-27.2; p = 0.024), folate (OR = 4.02; 1.87-8.66; p < 0.001), and with the presence of ≥ 2 micronutrient deficiencies (OR = 2.31; 1.21-4.42; p = 0.01).

CONCLUSIONS

Micronutrient deficiencies are common in patients with severe obesity undergoing BS, especially when inflammation is present. In the presence of increased CRP values before surgery, it might be advisable to search for possible multiple micronutrient deficiencies.

Focal Recurrent Copy Number Alterations Characterize Disease Relapse in High Grade Serous Ovarian Cancer Patients with Good Clinical Prognosis: A Pilot Study

High grade serous ovarian cancer (HGSOC) retains high molecular heterogeneity and genomic instability, which currently limit the treatment opportunities. HGSOC patients receiving complete cytoreduction (R0) at primary surgery and platinum-based therapy may unevenly experience early disease relapse, in spite of their clinically favorable prognosis. To identify distinctive traits of the genomic landscape guiding tumor progression, we focused on the R0 patients of The Cancer Genome Atlas (TCGA) ovarian serous cystadenocarcinoma (TCGA-OV) dataset and classified them according to their time to relapse (TTR) from surgery. We included in the study two groups of R0-TCGA patients experiencing substantially different outcome: Resistant (R; TTR ≤ 12 months; n = 11) and frankly Sensitive (fS; TTR ≥ 24 months; n = 16). We performed an integrated clinical, RNA-Sequencing, exome and somatic copy number alteration (sCNA) data analysis. No significant differences in mutational landscape were detected, although the lack of BRCA-related mutational signature characterized the R group. Focal sCNA analysis showed a higher frequency of amplification in R group and deletions in fS group respectively, involving cytobands not commonly detected by recurrent sCNA analysis. Functional analysis of focal sCNA with a concordantly altered gene expression identified in R group a gain in Notch, and interferon signaling and fatty acid metabolism. We are aware of the constraints related to the low number of OC cases analyzed. It is worth noting, however, that the sCNA identified in this exploratory analysis and characterizing Pt-resistance are novel, deserving validation in a wider cohort of patients achieving complete surgical debulking.

Helicobacter pylori and nutrition: a bidirectional communication

Helicobacter pylori (HP) is a gram-negative flagellated pathogen acid-resistant bacterium; it belongs to the order Campylobacterales that is wide spread all over the world, infecting more than 50% of the world population. HP infection is etiologically associated with non-atrophic and atrophic gastritis, peptic ulcer and with 3 to 6-fold increased relative risk for developing gastric adenocarcinoma and mucosa-associated lymphoid tissue (MA LT) lymphoma. For this reason HP is recognized by the World Health Organization as a Class I human carcinogen. In the last years a lot of studies clarified the role of this pathogen in nutrition and metabolism; particularly, it has been shown that it is able to induce malabsorption of several nutrients like iron, cobalamin, vitamin C and vitamin E, with strong consequences on nutritional status. Interesting, this bacterium is able to produce different biological effects on hormones like ghrelin and leptin controlling both appetite and growth, mostly depending on the time of acquisition of the infection and of its treatment. In this review, the authors focused their attention on nutritional effects of HP infection and particularly on the role that diet, food, plants and specific nutrients can play in its treatment, considering that HP eradication rates, with standard triple-therapy, have fallen to a low level in the last years.

The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial-mesenchymal transition, and immune response

BACKGROUND

Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive, and poorly investigated simple sarcoma with a low frequency of genetic deregulation other than an Ewing sarcoma RNA binding protein 1 (EWSR1)-Wilm's tumor suppressor (WT1) translocation. We used whole-exome sequencing to interrogate six consecutive pre-treated DSRCTs whose gene expression was previously investigated.

METHODS

DNA libraries were prepared from formalin-fixed, paraffin-embedded archival tissue specimens following the Agilent SureSelectXT2 target enrichment protocol and sequenced on Illumina NextSeq 500. Raw sequence data were aligned to the reference genome with Burrows-Wheeler Aligner algorithm. Somatic mutations and copy number alterations (CNAs) were identified using MuTect2 and EXCAVATOR2, respectively. Biological functions associated with altered genes were investigated through Ingenuity Pathway Analysis (IPA) software.

RESULTS

A total of 137 unique somatic mutations were identified: 133 mutated genes were case-specific, and 2 were mutated in two cases but in different positions. Among the 135 mutated genes, 27% were related to two biological categories: DNA damage-response (DDR) network that was also identified through IPA and mesenchymal-epithelial reverse transition (MErT)/epithelial-mesenchymal transition (EMT) already demonstrated to be relevant in DSRCT. The mutated genes in the DDR network were involved in various steps of transcription and particularly affected pre-mRNA. Half of these genes encoded RNA-binding proteins or DNA/RNA-binding proteins, which were recently recognized as a new class of DDR players. CNAs in genes/gene families, involved in MErT/EMT and DDR, were recurrent across patients and mostly segregated in the MErT/EMT category. In addition, recurrent gains of regions in chromosome 1 involving many MErT/EMT gene families and loss of one arm or the entire chromosome 6 affecting relevant immune-regulatory genes were recorded.

CONCLUSIONS

The emerging picture is an extreme inter-tumor heterogeneity, characterized by the concurrent deregulation of the DDR and MErT/EMT dynamic and plastic programs that could favour genomic instability and explain the refractory DSRCT profile.

Abstract 2753: Mutational profiles from targeted NGS combine with miRNA-based liquid biopsy to predict survival in LDCT screening-detected lung cancers

In order to increase cost-effectiveness of low-dose computed tomography (LDCT) lung cancer screening programs, a change in the management of screening-detected lung tumors should be considered. The higher percentage and the better 5-year overall survival of early stage tumors in LDCT screening series than in clinical practice argue in favor of screening programs. On the other hand, the overall limited reduction of mortality observed in screening trials with an observational control arm suggests that some of the screening-detected early stage tumors might be over-diagnosed. In our Institution we are trying to address this issue by the development of complementary biomarkers able to improve detection of aggressive disease. Targeted next-generation sequencing was performed in 94 LDCT screening-detected lung tumors resected from subjects participating in 3 screening trials enrolling 9,248 volunteers. Mutation profile was associated with subjects’ clinicopathologic features and with the risk profile of a plasma microRNA signature classifier (MSC). Using data available through The Cancer Genome Atlas database (TCGA), we compared the mutations of a selected set of non-small cell lung cancer (NSCLC) cases detected in standard clinical practice to LDCT screening-detected NSCLC cases. The 5-year overall survival (OS) of screening patients with and without mutations in the tumors was 64% and 100%, respectively (p=0.019). By combining the mutational status with the MSC, patients were stratified into 3 groups with 5-year OS ranging from 41% to 96% (p&lt;0.0001) and the prognostic value was significant even when controlling for stage (p=0.017). The comparison with TCGA data revealed a higher number of non-mutated NSCLC among screening patients (21% vs. 13%), despite the similar spectrum and frequency of mutations. In addition, the difference in 5-year OS between subjects with and without mutations was exclusively detected in screening patients. The mutation profile of screening-detected tumors, while similar to that of clinically detected tumors, was a strong predictor of OS. The combination of tumor mutational status and a circulating miRNA-based risk classifier predicts tumor aggressiveness and clinical outcome and may find rapid application in LDCT screening programs.

Citation Format: Mattia Boeri, Carla Verri, Cristina Borzi, Todd Holscher, Matteo Dugo, Andrea Devecchi, Elisa Romeo, Stefano Sestini, Paola Suatoni, Ugo Pastorino, Gabriella Sozzi. Mutational profiles from targeted NGS combine with miRNA-based liquid biopsy to predict survival in LDCT screening-detected lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2753. doi:10.1158/1538-7445.AM2017-2753

Mutational Profile from Targeted NGS Predicts Survival in LDCT Screening-Detected Lung Cancers

Background:

The issue of overdiagnosis in low-dose computed tomography (LDCT) screening trials could be addressed by the development of complementary bio-markers able to improve detection of aggressive disease. The mutation profile of LDCT screening–detected lung tumors is currently unknown.

Methods:

Targeted next-generation sequencing was performed on 94 LDCT screening–detected lung tumors. Associations with clinicopathologic features, survival, and the risk profile of a plasma microRNA signature classifier were analyzed.

Results:

The mutational spectrum and frequency observed in screening series was similar to that reported in public data sets, although a larger number of tumors without mutations in driver genes was detected. The 5-year overall survival (OS) rates of patients with and without mutations in the tumors were 66% and 100%, respectively (p = 0.015). By combining the mutational status with the microRNA signature classifier risk profile, patients were stratified into three groups with 5-year OS rates ranging from 42% to 97% (p < 0.0001) and the prognostic value was significant after controlling for stage (p = 0.02).

Conclusion:

Tumor mutational status along with a microRNA-based liquid biopsy can provide additional information in planning clinical follow-up in lung cancer LDCT screening programs.

Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

Background

Androgen insensitivity syndrome (AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor (AR) gene. A variety of tumors have been reported in association with AIS, but no cases with colorectal cancer (CRC) have been described.

Case presentation

Here, we present a male patient with AIS who developed multiple early-onset CRCs and his pedigree. His first cousin was diagnosed with AIS and harbored the same AR gene mutation, but with no signs of CRC. The difference in clinical management for the two patients was that testosterone treatment was given to the proband for a much longer time compared with the cousin. The CRC family history was negative, and no germline mutations in well-known CRC-related genes were identified. A single nucleotide polymorphism array revealed a microduplication on chromosome 22q11.22 that encompassed a microRNA potentially related to CRC pathogenesis. In the proband, whole exome sequencing identified a polymorphism in an oncogene and 13 rare loss-of-function variants, of which two were in CRC-related genes and four were in genes associated with other human cancers.

Conclusions

By pathway analysis, all inherited germline genetic events were connected in a unique network whose alteration in the proband, together with continuous testosterone stimulation, may have played a role in CRC pathogenesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s40880-016-0115-1) contains supplementary material, which is available to authorized users.

[1997 FIVNAT general balance]

In 1997, the French National Register on in vitro fertilization, FIVNAT, has collected information on 3,854 initiated cycles and 36,583 oocyte recoveries, from which 61.2% were conventional IVF cycles and 38.6% were ICSI. For conventional IVF, the percentage of infertilities of tubal origin was 49.7%, whereas 45% of the recoveries involved a male factor. The stimulation regimen involved a GnRH in 95% of the cases mostly with a long blockage period (82.6%) which was associated to the highest pregnancy rate. The mean number of transferred embryos significantly decreased to 2.50 +/- 0.95 per transfer. Only 9.2% of the transfers involved more than 3 embryos, and were associated to a relatively poor pregnancy rate, confirming that they were preferently realised in couples with poor chances of pregnancy. Finally, the pregnancy rate per recovery (20.5%) and per transfer (26.0%) remained at the same level as in 1996.

FIVNAT. Influence of attempt rank in in vitro fertilization

The French national register on in vitro fertilization (IVF) FIVNAT, which has collected most of the oocyte pick-ups realised in France since 1986 has allowed us to build a cohort of 35,714 couples, of which the first recovery took place between 1990 and 1994 and followed up to a pregnancy or to the 31st of december, 1996. The per recovery clinical pregnancy rate decreased from 20.2% on the first attempt to 17.4% on the second, and to less than 13% after the sixth. This evolution existed whatever the women's age class or the infertility diagnosis. The women's age remained the most important factor, since the cumulative pregnancy rate decreased from 60% for women aged less than 35 years to 17% for those aged more than 41 years. Among the indications, male infertility using spouse's semen had the poorest prognosis, especially for women aged more than 41 years (9.6%) whereas male infertility using donor's semen among women aged less than 35 years was associated to the best results (68%). It must be noticed than a high percentage of unpregnant women did not come again for a further recovery (40% to 50%). Then, the crude cumulative birth rate (24.4%) was far below the theoretical cumulative one(54.2%).