Advancements in long-read genome sequencing technologies and algorithms

The recent advent of long read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), have led to substantial improvements in accuracy and computational cost in sequencing genomes. However, de novo whole-genome assembly still presents significant challenges related to the quality of the results. Pursuing de novo whole-genome assembly remains a formidable challenge, underscored by intricate considerations surrounding computational demands and result quality. As sequencing accuracy and throughput steadily advance, a continuous stream of innovative assembly tools floods the field. Navigating this dynamic landscape necessitates a reasonable choice of sequencing platform, depth, and assembly tools to orchestrate high-quality genome reconstructions. This comprehensive review delves into the intricate interplay between cutting-edge long read sequencing technologies, assembly methodologies, and the ever-evolving field of genomics. With a focus on addressing the pivotal challenges and harnessing the opportunities presented by these advancements, we provide an in-depth exploration of the crucial factors influencing the selection of optimal strategies for achieving robust and insightful genome assemblies.

Overall survival from tebentafusp versus nivolumab plus ipilimumab in first-line metastatic uveal melanoma: a propensity score-weighted analysis

BACKGROUND

Tebentafusp demonstrated a superior overall survival (OS) benefit [hazard ratio (HR) 0.51] compared to investigator's choice (82% pembrolizumab) in a randomized, phase III trial (IMCgp100-202; N = 378) in untreated metastatic uveal melanoma (mUM). The 1-year OS rates for tebentafusp and pembrolizumab were 73% and 59%, respectively. In the single-arm GEM1402 (N = 52), the 1-year OS rate for nivolumab plus ipilimumab (N+I) in mUM was 52%. Due to limitations in conducting randomized trials in mUM, we compared OS on tebentafusp or pembrolizumab (IMCgp100-202) to N+I (GEM1402) in untreated mUM using propensity scoring methods.

PATIENTS AND METHODS

Analyses were adjusted using propensity score-based inverse probability of treatment weighting (IPTW), balancing age, sex, baseline lactate dehydrogenase (LDH), baseline alkaline phosphatase, disease location, Eastern Cooperative Oncology Group status, and time from primary diagnosis to metastasis. OS was assessed using IPT-weighted Kaplan-Meier and Cox proportional hazard models. Sensitivity analyses using alternative missing data and weights methods were conducted.

RESULTS

The primary IPTW analysis included 240 of 252 patients randomized to tebentafusp from IMCgp100-202 and 45 of 52 N+I-treated patients from GEM-1402. Key baseline covariates, including LDH, were generally well balanced before weighting. The IPTW-adjusted OS favored tebentafusp, HR 0.52 [95% confidence interval (CI) 0.35-0.78]; 1-year OS was 73% for tebentafusp versus 50% for N+I. Sensitivity analyses showed consistent superior OS for tebentafusp with all IPTW HRs ≤0.61. IPTW analysis of pembrolizumab versus N+I showed no significant difference in OS (HR 0.72; 95% CI 0.50-1.06).

CONCLUSIONS

Tebentafusp was previously shown to provide an OS benefit compared to checkpoint inhibitors or chemotherapy in untreated mUM. Propensity score analysis demonstrated a similar OS benefit for tebentafusp compared with N+I. These data further support tebentafusp as the standard of care in previously untreated human leukocyte antigen (HLA)-A∗02:01+ adult patients with mUM.

Comparing assembly strategies for third-generation sequencing technologies across different genomes

The recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computational cost and the quality of the results. Accordingly, sequencing accuracy and throughput continue to improve, and many tools are constantly emerging. Therefore, selecting the correct sequencing platform, the proper sequencing depth and the assembly tools are necessary to perform high-quality assembly. This paper evaluates the primary assembly reconstruction from recent hybrid and non-hybrid pipelines on different genomes. We find that using PacBio high-fidelity long-read (HiFi) plays an essential role in haplotype construction with respect to ONT reads. However, we observe a substantial improvement in the correctness of the assembly from high-fidelity ONT datasets and combining it with HiFi or short-reads.

The SMC-like RecN protein is at the crossroads of several genotoxic stress responses in Escherichia coli

Introduction

DNA damage repair (DDR) is an essential process for living organisms and contributes to genome maintenance and evolution. DDR involves different pathways including Homologous recombination (HR), Nucleotide Excision Repair (NER) and Base excision repair (BER) for example. The activity of each pathway is revealed with particular drug inducing lesions, but the repair of most DNA lesions depends on concomitant or subsequent action of the multiple pathways.

Methods

In the present study, we used two genotoxic antibiotics, mitomycin C (MMC) and Bleomycin (BLM), to decipher the interplays between these different pathways in E. coli. We combined genomic methods (TIS and Hi-SC2) and imaging assays with genetic dissections.

Results

We demonstrate that only a small set of DDR proteins are common to the repair of the lesions induced by these two drugs. Among them, RecN, an SMC-like protein, plays an important role by controlling sister chromatids dynamics and genome morphology at different steps of the repair processes. We further demonstrate that RecN influence on sister chromatids dynamics is not equivalent during the processing of the lesions induced by the two drugs. We observed that RecN activity and stability requires a pre-processing of the MMC-induced lesions by the NER but not for BLM-induced lesions.

Discussion

Those results show that RecN plays a major role in rescuing toxic intermediates generated by the BER pathway in addition to its well-known importance to the repair of double strand breaks by HR.

A genome-wide association study of survival in patients with sepsis

BACKGROUND

Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction and has a high mortality rate in adult intensive care units. Most genetic studies have identified gene variants associated with development and outcomes of sepsis focusing on biological candidates. We conducted the first genome-wide association study (GWAS) of 28-day survival in adult patients with sepsis.

METHODS

This study was conducted in two stages. The first stage was performed on 687 European sepsis patients from the GEN-SEP network and 7.5 million imputed variants. Association testing was conducted with Cox regression models, adjusting by sex, age, and the main principal components of genetic variation. A second stage focusing on the prioritized genetic variants was performed on 2,063 ICU sepsis patients (1362 European Americans and 701 African-Americans) from the MESSI study. A meta-analysis of results from the two stages was conducted and significance was established at p < 5.0 × 10-8. Whole-blood transcriptomic, functional annotations, and sensitivity analyses were evaluated on the identified genes and variants.

FINDINGS

We identified three independent low-frequency variants associated with reduced 28-day sepsis survival, including a missense variant in SAMD9 (hazard ratio [95% confidence interval] = 1.64 [1.37-6.78], p = 4.92 × 10-8). SAMD9 encodes a possible mediator of the inflammatory response to tissue injury.

INTERPRETATION

We performed the first GWAS of 28-day sepsis survival and identified novel variants associated with reduced survival. Larger sample size studies are needed to better assess the genetic effects in sepsis survival and to validate the findings.

Admixture Mapping of Sepsis in European Individuals With African Ancestries

Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10⁻⁴; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10⁻⁴; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.

Fertility sparing treatment in patients with endometrial cancer (FERT-ENC): a multicentric retrospective study from the Spanish Investigational Network Gynecologic Oncology Group (SPAIN-GOG)

OBJECTIVE

The primary objective was to evaluate the response rate of conservative treatment for endometrial cancer, and the secondary objective was to assess oncological, fertility and obstetric outcomes in patients who underwent fertility preservation treatment.

MATERIAL AND METHODS

This multicentre, observational, retrospective study evaluated endometrial cancer patients who underwent fertility-sparing treatment in Spanish centres between January 2010 and January 2020. Seventy-three patients with stage IA endometrioid adenocarcinoma of the uterus were included in the study.

RESULTS

The levonorgestrel intrauterine device (LNG-IUD) was the most common fertility-sparing treatment (53.4%), followed by megestrol acetate (20.5%) and medroxyprogesterone acetate (16.4%). During the 24-month follow-up period, the rate of complete response to fertility-sparing management was 74% (n = 54), and 8.2% (n = 6) of patients presented a partial response. Additionally, 13 (17.8%) patients presented with persistent disease and six (8.2%) relapsed after response. The LNG-IUD was associated with a higher complete response rate than the other methods (87.2 vs. 58.8%; p = 0.01). Surgical treatment (at least hysterectomy) was performed in 44 (60.3%) patients as the end of fertility-sparing treatment. Four (5.5%) patients presented relapse after surgery, associated with final FIGO stage III (p = 0.036), myometrial invasion > 50% (p = 0.018) and final tumour grade 2-3 (p = 0.018). The mean follow-up period was 57.8 (range 6-159) months. The 5-year relapse-free survival and overall survival rates were 92.6% [95% CI (81.3, 97.2)] and 93.5% [95% CI (80.7, 97.9)], respectively. During follow-up, three patients (4.1%) died of the disease after completion of surgical treatment. Up to 50.7% of patients included in the study attempted to get pregnant. Of these, the rate of pregnancy was 81.1% (n = 30/37), and reproductive techniques were used for this purpose in 78.4% of cases.

CONCLUSIONS

Fertility-sparing management presented a high response rate in patients with endometrial cancer. LNG-IUD was associated with a better response rate compared to the other treatment options. Moreover, in patients using this management method, pregnancy could be achieved using reproductive techniques.

Plesiomonas shigelloides, an Atypical Enterobacterales with a Vibrio-related secondary chromosome

About 10% of bacteria have a multichromosome genome with a primary replicon of bacterial origin, called the chromosome, and other replicons of plasmid origin, the chromids. Studies on multichromosome bacteria revealed potential points of coordination between the replication/segregation of chromids and the progression of the cell cycle. For example, replication of the chromid of Vibrionales (called Chr2) is initiated upon duplication of a sequence carried by the primary chromosome (called Chr1), in such a way that replication of both replicons is completed synchronously. Also, Chr2 uses the Chr1 as a scaffold for its partition in the daughter cells. How many of the features detected so far are required for the proper integration of a secondary chromosome in the cell cycle? How many more features remain to be discovered? We hypothesized that critical features for the integration of the replication/segregation of a given chromid within the cell cycle program would be conserved independently of the species in which the chromid has settled. Hence, we searched for a chromid related to that found in Vibrionales outside of this order. We identified one in Plesiomonas shigelloides, an aquatic and pathogenic enterobacterium that diverged early within the clade of Enterobacterales. Our results suggest that the chromids present in P. shigelloides and Vibrionales derive from a common ancestor. We initiated in silico genomic and proteomic comparative analyses of P. shigelloides, Vibrionales, and Enterobacterales that enabled us to establish a list of features likely involved in the maintenance of the chromid within the host cell cycle.

Whole-Blood Mitochondrial DNA Copies Are Associated With the Prognosis of Acute Respiratory Distress Syndrome After Sepsis

Acute respiratory distress syndrome (ARDS) is an inflammatory process of the lungs that develops primarily in response to pulmonary or systemic sepsis, resulting in a disproportionate death toll in intensive care units (ICUs). Given its role as a critical activator of the inflammatory and innate immune responses, previous studies have reported that an increase of circulating cell-free mitochondrial DNA (mtDNA) is a biomarker for fatal outcome in the ICU. Here we analyzed the association of whole-blood mtDNA (wb-mtDNA) copies with 28-day survival from sepsis and sepsis-associated ARDS. We analyzed mtDNA data from 687 peripheral whole-blood samples within 24 h of sepsis diagnosis from unrelated Spanish patients with sepsis (264 with ARDS) included in the GEN-SEP study. The wb-mtDNA copies were obtained from the array intensities of selected probes, with 100% identity with mtDNA and with the largest number of mismatches with the nuclear sequences, and normalized across the individual-probe intensities. We used Cox regression models for testing the association with 28-day survival. We observed that wb-mtDNA copies were significantly associated with 28-day survival in ARDS patients (hazard ratio = 3.65, 95% confidence interval = 1.39–9.59, p = 0.009) but not in non-ARDS patients. Our findings support that wb-mtDNA copies at sepsis diagnosis could be considered an early prognostic biomarker in sepsis-associated ARDS patients. Future studies will be needed to evaluate the mechanistic links of this observation with the pathogenesis of ARDS.

SEOM clinical guideline for the management of cutaneous melanoma (2020)

Melanoma affects about 6000 patients a year in Spain. A group of medical oncologists from Spanish Society of Medical Oncology (SEOM) and Spanish Multidisciplinary Melanoma Group (GEM) has designed these guidelines to homogenize the management of these patients. The diagnosis must be histological and determination of BRAF status has to be performed in patients with stage ≥ III. Stage I–III resectable melanomas will be treated surgically. In patients with stage III melanoma, adjuvant treatment with immunotherapy or targeted therapy is also recommended. Patients with unresectable or metastatic melanoma will receive treatment with immunotherapy or targeted therapy, the optimal sequence of these treatments remains unclear. Brain metastases require a separate consideration, since, in addition to systemic treatment, they may require local treatment. Patients must be followed up closely to receive or change treatment as soon as their previous clinical condition changes, since multiple therapeutic options are available.

Protocol for High-Throughput Analysis of Sister-Chromatids Contacts

Sister chromatid interactions are a key step to ensure the successful segregation of sister chromatids after replication. Our knowledge about this phenomenon is mostly based on microscopy approaches, which have some constraints such as resolution limit and the impossibility of studying several genomic positions at the same time. Here, we present a protocol for Hi-SC2, a high-throughput sequencing-based method, to monitor sister chromatid contacts after replication at high resolution throughout the genome, which we applied to study cohesion in Vibrio cholerae.

For complete details on the use and execution of this protocol, please refer to Espinosa et al. (2020).

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Method to analyze sister chromatid contacts at high resolution

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Step-by-step protocol from cell culture to bioinformatics analysis

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Protocol easy to adapt to different organisms

Incidence of venous thromboembolic events in cancer patients receiving immunotherapy: a single-institution experience

BACKGROUND

Cancer and cancer therapies have been associated with an increased incidence of venous thromboembolic events (VTE). However, the incidence of VTE in patients on immunotherapy has not been well characterized. The aim of this study was to assess the incidence of VTE in cancer patients receiving immunotherapy and ascertain its prognostic utility.

MATERIALS AND METHODS

We conducted a single-institution retrospective study, including all cancer patients treated with anti-Programmed cell Death 1 (PD-1), anti-Programmed cell Death Ligand-1 (PD-L1), anti-Cytotoxic T-Lymphocyte-Associated Protein 4 (CTLA4), a combination of anti-PD-1/anti-PD-L1 and anti-CTLA4 or a combination including any of these drugs with chemotherapy, antiangiogenic agents or both between June 2013 and April 2019 at La Paz University Hospital, Madrid (Spain).

RESULTS

We selected 229 patients. VTE occurred in 16 of 229 patients (7%). VTE occurred more frequently in patients with lung cancer followed by melanoma. Female sex and melanoma were independently associated with an increased risk of VTE. 12 of 16 VTE (75%) were symptomatic. Progressive disease to immunotherapy [HR 31.60 (95% CI 11.44-87.22), p = 0.00], lung cancer [HR 2.55 (95% CI 1.34-4.86), p = 0.00] and melanoma [HR 2.42 (1.20-4.86), p = 0.01] were independently associated with shorter OS. VTE occurrence was not independently associated with shorter OS [HR 1.33 (95% CI 0.63-2.80), p = 0.44].

CONCLUSIONS

The incidence of VTE in cancer patients receiving immunotherapy in our study appeared to be similar to the incidence previously reported in other series of cancer patients treated with systemic therapies. VTE occurrence did not correlate with the prognosis. Further and prospective studies are needed to derive definitive conclusions.

Bicuspid aortic valve: prompt identification of high-risk groups in a heterogeneous disease

Background

Bicuspid aortic valve (BAV) is a congenital heart disease that can be associated with aortic and/or valve complications. Although most BAV are predisposed to progressive calcification, little is known on variables related to significant valvular dysfunction. BAV is a heterogeneous disease, therefore it is important to identify high-risk groups for a closer follow- up and timely intervention.

Objective

Identify the main determinants of primary cardiovascular events (aortic valve replacement, aortic surgery and death) in a cohort of adults with BAV.

Methods

We included 325 consecutive patients with non-syndromatic BAV (2010–2019) referred to our hospital (3rd level). Clinical information was prospectively collected. All patients underwent serial echocardiograms and Cardiac CT was available in 125 patients (38%). We performed univariate and multivariate analyses and Kaplan-Meyer survival analysis with log-rank test. A p-value &lt;0.05 was considered significant.

Results

325 patients (44.4±15.3 years, 73% men), right–left coronary cusp fusion (RL) in 79%,and presence of raphe in 77%. 100 patients (31.2%) had significant aortic valve dysfunction and 103 (31.7%) had aortic dialatation (&gt;40mm) at the onset of the follow-up. Twenty-nine patients required cardiac surgery (8.9%, mainly symptomatic severe aortic stenosis with aortic valve replacement)and 3 died (1%) during a follow-up of 6.3±1.2 years. Patients with at least 2 of the following determinants at baseline: aortic valve prolapse, aortic valve calcification &gt;1, age &gt;50 years and/or aorta &gt;45mm had higher risk of major cardiovascular events during follow-up (Chi2 for log rank test=27,229 p=0,000005).

Conclusions

In this study population of young adults with BAV we observed a high incidence of events related to the BAV. Age&gt;50 years, aortic valve calcification, aortic valve prolapse and aortic dilatation were independently associated with primary cardiac events. Despite significant BAV heterogeneity, the identification of risk factors may help to stratify the risk of valvular dysfunction, aortic dilatation and major cardiovascular events.

BAV: Risk factors for cardiac surgery

Funding Acknowledgement

Type of funding source: None

High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts

Sister-chromatid cohesion describes the orderly association of newly replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and faithful transmission of genetic information. Cohesion is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected by many processes. Current knowledge on cohesion has been mainly gained by fluorescence microscopy observation. However, the resolution limit of microscopy and the restricted number of genomic positions that can be simultaneously visualized considerably hampered progress. Here, we present a high-throughput methodology to monitor sister-chromatid contacts (Hi-SC2). Using the multi-chromosomal Vibrio cholerae bacterium as a model, we show that Hi-SC2 permits to monitor local variations in sister-chromatid cohesion at a high resolution over a whole genome.

Bevacizumab in recurrent ovarian cancer: could it be particularly effective in patients with clear cell carcinoma?

PURPOSE

Treatment of recurrent ovarian carcinoma is a challenge, particularly for the clear cell (CCC) subtype. However, there is a preclinical rationale that these patients could achieve a benefit from antiangiogenic therapy. To assess this hypothesis, we used the growth modulation index (GMI), which represents an intrapatient comparison of two successive progression-free survival (PFS).

METHODS

We conducted a retrospective real-world study performed on 34 patients with recurrent ovarian cancer, treated with bevacizumab-containing regimens from January 2009 to December 2017. The primary endpoint was GMI. An established cut-off > 1.33 was defined as a sign of drug activity.

RESULTS

73.5% of patients had high-grade serous ovarian carcinoma (HGSOC), and 17.7% had CCC; 70.6% of patients received carboplatin/gemcitabine/bevacizumab, and 29.4% received weekly paclitaxel/bevacizumab. According to histological subtype, the overall response rate and median PFS were 52% and 14 months for HGSOC and 83.3% and 20 months for CCC, respectively. The overall population median GMI was 0.99; it was 0.95 and 2.36 for HGSOC and CCC, respectively. CCC subtype was significantly correlated with GMI > 1.33 (odds ratio 41.67; 95% confidence interval 3.6-486.94; p = .03).

CONCLUSION

Adding bevacizumab to chemotherapy in recurrent CCC is associated with a remarkable benefit in this cohort. The efficacy of antiangiogenic drugs in CCC warrants further prospective evaluation.

Is the fast-track process efficient and safe for older adults admitted to the emergency department?

BACKGROUND

The efficiency of the fast-track (FT) process in the management of patients in Emergency Departments is well demonstrated, but there is a lack of research focused on older adults. The aim of our study was to verify whether the FT process is efficient and safe for older adults admitted to ED.

METHODS

Observational case-control single-centre study.

RESULTS

Five hundred four cases and 504 controls were analysed. The mean age was 75 years, and there was a predominance of women. In total 96% of subjects were classified with a "less-urgent" tag. The length of stay was significantly lower in the fast-track group than in the control group (median 178 min, interquartile range 184 min, and 115 min, interquartile range 69 min, respectively, p < 0.001), as well as the time spent between the ED physician's visit and patient discharge (median 78 min, interquartile range 120 min, and median 3 min, interquartile range 6 min, respectively, p < 0.001). There weren't any increases in the number of unplanned readmissions within 48 h, 7 days and 30 days.

CONCLUSIONS

The fast-track appears to be an efficient and safe strategy to improve the management of older adults admitted to the ED with minor complaints.

Sepsis-associated acute respiratory distress syndrome in individuals of European ancestry: a genome-wide association study

BACKGROUND

Acute respiratory distress syndrome (ARDS) is a lung inflammatory process caused mainly by sepsis. Most previous studies that identified genetic risks for ARDS focused on candidates with biological relevance. We aimed to identify novel genetic variants associated with ARDS susceptibility and to provide complementary functional evidence of their effect in gene regulation.

METHODS

We did a case-control genome-wide association study (GWAS) of 1935 European individuals, using patients with sepsis-associated ARDS as cases and patients with sepsis without ARDS as controls. The discovery stage included 672 patients admitted into a network of Spanish intensive care units between January, 2002, and January, 2017. The replication stage comprised 1345 individuals from two independent datasets from the MESSI cohort study (Sep 22, 2008-Nov 30, 2017; USA) and the VISEP (April 1, 2003-June 30, 2005) and MAXSEP (Oct 1, 2007-March 31, 2010) trials of the SepNet study (Germany). Results from discovery and replication stages were meta-analysed to identify association signals. We then used RNA sequencing data from lung biopsies, in-silico analyses, and luciferase reporter assays to assess the functionallity of associated variants.

FINDINGS

We identified a novel genome-wide significant association with sepsis-associated ARDS susceptibility (rs9508032, odds ratio [OR] 0·61, 95% CI 0·41-0·91, p=5·18 × 10^-8) located within the Fms-related tyrosine kinase 1 (FLT1) gene, which encodes vascular endothelial growth factor receptor 1 (VEGFR-1). The region containing the sentinel variant and its best proxies acted as a silencer for the FLT1 promoter, and alleles with protective effects in ARDS further reduced promoter activity (p=0·0047). A literature mining of all previously described ARDS genes validated the association of vascular endothelial growth factor A (VEGFA; OR 0·55, 95% CI 0·41-0·73; p=4·69 × 10^-5).

INTERPRETATION

A common variant within the FLT1 gene is associated with sepsis-associated ARDS. Our findings support a role for the vascular endothelial growth factor signalling pathway in ARDS pathogenesis and identify VEGFR-1 as a potential therapeutic target.

FUNDING

Instituto de Salud Carlos III, European Regional Development Funds, Instituto Tecnológico y de Energías Renovables.

Abstract P5-12-14: A pilot study of metabolomics biomarkers in breast cancer tumors treated with neoadjuvant therapy

Introduction

Breast cancer is one of the most prevalent cancers in the world. Traditionally, early breast cancer treatment is based on surgery and, after surgery, hormone treatment or chemotherapy. However, the neoadjuvant treatment is increasingly used. Metabolomics is the most recent “omics” which allows quantify metabolites into blood patient samples. Coupled with computational analyses it could be possible to study differential metabolomics patterns and associate them with neoadjuvant response.

Material and methods

Blood plasma samples from patients with breast cancer treated with neoadjuvant chemotherapy were used to perform metabolomics experiments. One sample before the treatment (basal) and one sample after the chemotherapy (post-treatment) were analyzed and clinical data regarding response (complete response or partial response) was also collected. Metabolomics experiments were performed using liquid chromatography coupled with mass-spectrometry. Bayesian network and class comparison analyses were used to establish differential metabolic patterns between conditions. Additionally, a response prediction model based on logistic regression was build using metabolomics data from basal samples.

Results and discussion

A network showing the relationships between metabolites was build. Comparing metabolite measurements between complete response and partial response tumors in basal samples, 19 metabolites showed a differential quantification between both types of responses. Moreover, one of these metabolites is linoleic acid, previously described as a biomarker of complete response in neoadjuvant treatment in breast cancer. Using these 19 differential metabolites, a response predictive model was build. According to this model, it is possible to predict response to neoadjuvant treatment based on the amount of one metabolite, still only identified by its mass and charge. On the other hand, comparing basal and post-treatment samples, the network showed differential metabolomics patterns. These differential metabolites could be used as predictive biomarkers of response.

Conclusion

This study is a proof of concept that using a new “omics” technique such as metabolomics in blood samples, coupled with computational analyses, it is possible to identify differential metabolomics patterns between complete and partial response or basal and post-treatment samples and design predictive models of response These results could facilitate in the future the implementation of blood-based tests into the clinical routine.

Citation Format: Zamora P, Trilla-Fuertes L, Zapater-Moros A, Gámez-Pozo A, Prado-Vázquez G, Ferrer-Gómez M, Díaz- Almirón M, López Vacas R, Espinosa E, Fresno Vara JA. A pilot study of metabolomics biomarkers in breast cancer tumors treated with neoadjuvant therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-12-14.

Abstract P2-02-13: Computational metabolism modeling predicts risk of relapse in breast cancer patients

Introduction

Breast cancer is one of the most prevalent cancers in the world. In previous works we observed differences in glucose metabolism between breast cancer subtypes, suggesting that metabolism plays an important role in this disease. Flux Balance Analysis (FBA) is widely used to study metabolic networks, allowing predicting growth rates or the rate of production of a given metabolite.

Material and methods

Proteomics data from 96 breast cancer tumors were obtained applying a high-throughput proteomics approach to routinely archive formalin-fixed, paraffin-embedded tumor tissue. Proteomics tumor data were analyzed using the human metabolic reconstruction Recon2 and FBA. The tumor growth rate for each tumor was calculated. In order to analyze fluxes from the different metabolic pathways, flux activities were calculated as the sum of the fluxes of each reaction in each pathway defined in the Recon2. Then, flux activities were used to build prognostic models.

Results and discussion

Using the results obtained from FBA in the proteomics dataset, flux activities were calculated for each pathway. Employing these flux activities, a prognostic signature was built. Flux activities of vitamin A, tetrahydrobiopterin metabolism and beta-alanine metabolism pathways split our population into a low and a high risk group (p=0.044).

Conclusion

Vitamine A, beta-alanine and tetrahydrobiopterin metabolism flux activities could be used to predict relapse risk. Flux activities is a method proposed in a previous work to study response against drugs that now also demonstrated its utility in summarizing FBA data and is associated with prognosis.

Citation Format: Zamora P, Trilla-Fuertes L, Gámez-Pozo A, Prado-Vázquez G, Zapater-Moros A, Ferrer-Gómez M, Díaz- Almirón M, López Vacas R, Espinosa E, Fresno Vara JA. Computational metabolism modeling predicts risk of relapse in breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-02-13.

Coordination between replication, segregation and cell division in multi-chromosomal bacteria: lessons from Vibrio cholerae

Bacteria display a highly flexible cell cycle in which cell division can be temporally disconnected from the replication/segregation cycle of their genome. The accuracy of genetic transmission is enforced by restricting the assembly of the cell division apparatus to the low DNA-density zones that develop between the regularly spaced nucleoids originating from the concurrent replication and segregation of genomic DNA. In most bacteria, the process is simplified because the genome is encoded on a single chromosome. This is notably the case in Escherichia coli, the most well studied bacterial model organism. However, ~10% of bacteria have domesticated horizontally acquired mega-plasmids into extra-numerous chromosomes. Most of our current knowledge on the cell cycle regulation of multi-chromosomal species derives from the study of replication, segregation and cell division in Vibrio cholerae, the agent of the deadly epidemic human diarrheal disease cholera. A nicety of this model is that it is closely related to E. coli in the phylogenetic tree of bacteria. Here, we review recent findings on the V. cholerae cell cycle in the context of what was previously known on the E. coli cell cycle.

HIV Disease Progression: Overexpression of the Ectoenzyme CD38 as a Contributory Factor?

Despite abundant evidence associating CD38 overexpression and CD4 T cell depletion in HIV infection, no causal relation has been investigated. To address this issue, a series of mechanisms are proposed, supported by evidence from different fields, by which CD38 overexpression can facilitate CD4 T cell depletion in HIV infection. According to this model, increased catalytic activity of CD38 may reduce CD4 T cells' cytoplasmic nicotin-amide adenine dinucleotide (NAD), leading to a chronic Warburg effect. This will reduce mitochondrial function. Simultaneously, CD38's catalytic products ADPR and cADPR may be transported to the cytoplasm, where they can activate calcium channels and increase cytoplasmic Ca2+ concentrations, further altering mitochondrial integrity. These mechanisms will decrease the viability and regenerative capacity of CD4 T cells. These hypotheses can be tested experimentally, and might reveal novel therapeutic targets. Also see the video abstract here https://youtu.be/k1LTyiTKPKs.

[The importance of semiology and biochemistry in the diagnostic management of a peroxisomal biogenesis disorder]

INTRODUCTION

Peroxisomal biogenesis disorders are due to mutations in the PEX genes, which code for peroxins that are required for peroxisomal biogenesis. Clinically, they are expressed as a Zellweger syndrome spectrum, and there is a wide phenotypic variety. They are diagnosed biochemically, and confirmation is molecular. The aim of this illustrative case is to highlight the importance of the clinical features and biochemical testing in the management of a peroxisomal disease.

CASE REPORT

A 3-year-old boy with neonatal hypotonia, overall developmental delay and failure to thrive and a pattern of hypomyelinating leukodystrophy in brain resonance. The suspected diagnosis was a disorder affecting the biogenesis of the peroxisomes due to having found a variant with an uncertain meaning in PEX5. The clinical features, the biochemical studies and critical analysis, however, made this diagnosis unlikely. Emphasis is placed on the management that must be applied when a Zellweger syndrome spectrum is suspected.

CONCLUSION

In the case reported here, a peroxisomal biogenesis disorder was suspected owing to an exome sequencing which, on being critically analysed together with the clinical features and the biochemical findings, made a peroxisomal disease very unlikely. In cases of clinical suspicion, backed up by neuroimaging, the main diagnostic management must be based on the biochemistry analysis. Although confirmation is molecular, these tests must be interpreted with caution.

SEOM clinical guideline for the management of malignant melanoma (2017)

All melanoma suspected patients must be confirmed histologically and resected. Sentinel node biopsy must be done when tumor is over 1 mm or if less with high-risk factors. Adjuvant therapy with interferon could be offered for patients with high-risk melanoma and in selected cases radiotherapy can be added. Metastatic melanoma treatment is guided by mutational BRAF status. BRAF wild type patients must receive anti-PD1 containing therapy and BRAF mutated patients BRAF/MEK inhibitors or anti-PD1 containing therapy. Up to 10 years follow up is reasonable for melanoma patients with dermatologic examinations and physical exams.