A 3\u27UTR KRAS-variant as a biomarker of poor outcome and platinum chemotherapy resistance in ovarian cancer

Purpose: Ovarian cancer has a poor prognosis, yet pathologic and clinical data do not accurately predict which patients will ultimately succumb to their disease. We previously reported an association between rs61764370, a germline functional variant in the 3\u27UTR of the KRAS oncogene, and epithelial ovarian cancer (EOC) risk. Here we evaluate this variant as a biomarker of clinical outcome and chemotherapy resistance in EOC. Patients and Methods: Four groups of EOC patients with complete clinical data were genotyped for the KRAS-variant and analyzed: Sporadic EOC patients (n=451); BRCA mutant EOC patients (n=79); EOC patients treated with neoadjuvant chemotherapy (n=122), and; EOC patients treated adjuvantly with platinum-based chemotherapy after cytoreductive surgery (n=292). Results: The KRAS-variant predicts for significantly worse survival for EOC patients over 55 years-old by multivariate Cox regression analysis (HR=1.71, 95% CI=1.09 - 2.69, p = 0.02). However, for the subgroup of EOC patients with known BRCA mutations, the KRAS-variant did not predict altered outcome (HR=0.994, CI=0.28-3.56, p=0.99). KRAS-variant positive EOC patients respond poorly to neoadjuvant carboplatin and paclitaxel chemotherapy, having significantly more residual disease remaining after surgery (OR=26.27, CI=1.56- 441.83, p=0.0232). In addition, EOC patients that harbor the KRAS-variant are more likely to be resistant to adjuvant platinum chemotherapy (OR=2.86, CI=1.13-7.23, p=0.026). Conclusions: These findings expand the potential importance of the KRAS-variant in EOC, from acting as a marker of risk to being a biomarker that predicts worse outcome, perhaps due to its association with platinum resistance. These data may ultimately help lead to treatment optimization and improved outcome for KRAS-variant positive EOC patients

Antimicrobial peptides as novel anti-tuberculosis therapeutics

"Available online 24 May 2016"Tuberculosis (TB), a disease caused by the human pathogen Mycobacterium tuberculosis, has recently joined HIV/AIDS as the world's deadliest infectious disease, affecting around 9.6 million people worldwide in 2014. Of those, about 1.2 million died from the disease. Resistance acquisition to existing antibiotics, with the subsequent emergence of Multi-Drug Resistant mycobacteria strains, together with an increasing economic burden, has urged the development of new anti-TB drugs. In this scope, antimicrobial peptides (AMPs), which are small, cationic and amphipathic peptides that make part of the innate immune system, now arise as promising candidates for TB treatment. In this review, we analyze the potential of AMPs for this application. We address the mechanisms of action, advantages and disadvantages over conventional antibiotics and how problems associated with its use may be overcome to boost their therapeutic potential. Additionally, we address the challenges of translational development from benchside to bedside, evaluate the current development pipeline and analyze the expected global impact from a socio-economic standpoint. The quest for more efficient and more compliant anti-TB drugs, associated with the great therapeutic potential of emerging AMPs and the rising peptide market, provide an optimal environment for the emergence of AMPs as promising therapies. Still, their pharmacological properties need to be enhanced and manufacturing-associated issues need to be addressed.Portuguese Foundation for Science and Technology (FCT) - UID/ BIO/04469/2013 unit ; COMPETE 2020 (POCI-01-0145-FEDER- 006684) ; SFRH/BPD/64958/2010Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Outcomes following cryoablation of stage IA non-small cell lung cancer in patients with and without interstitial lung disease: A retrospective single-center cohort study

Objective: To compare the safety and efficacy of cryoablation of treatment-naïve stage IA non-small cell lung cancer (NSCLC) in patients with and without interstitial lung disease (ILD). Materials and methods: This retrospective single-center cohort study evaluated 33 consecutive patients (24 females, median age 75 years, Eastern Cooperative Oncology Group performance score 0-3) with ILD (9 patients) and without ILD (24 patients) who underwent 39 percutaneous cryoablations to treat 42 stage IA (8th IASLC edition) NSCLC measuring 1.2 cm (range 0.5-2.6 cm) from 2018 to 2022. Presence of ILD was determined according to 2018 American Thoracic Society Criteria on pre-ablation CT scans. The primary outcome was 90-day adverse events graded by the Common Terminology Criteria for Adverse Events (CTCAE) v5.0. Secondary outcomes were hospital length of stay (LOS), local recurrence-free survival, overall survival, and the cumulative incidence of local recurrence with death as a competing risk. Results: Adverse events ranged from grade 1-3 and occurred more often in the non-ILD group (p <.001). No acute exacerbation of ILD or death occurred within 90 days after cryoablation. The median LOS was 1 day (interquartile range 1-2 days) and did not differ between groups. One patient with ILD and two patients without ILD died after 22, 26, and 27 months from causes unrelated to cryoablation. Median imaging follow-up was 11 months (range, 0-47 months) and three tumors (7%) showed local recurrence after 4, 17, and 22 months. No difference in the cumulative incidence of local recurrence (p =.56) was found. Among all patients, local recurrence-free survival on a per-tumor basis and overall survival were 97% and 100% at 1 year, respectively. Conclusion: Adverse events and local recurrence following percutaneous cryoablation of stage IA NSCLC did not differ between patients with and without ILD. No acute exacerbation of ILD or death within 90 days were observed

A 3′-untranslated region kras variant and triple-negative breast cancer: a case-control and genetic analysis

Background We previously identified a functional variant in a let-7 microRNA (miRNA) complementary site in the 3\u27-untranslated region of the KRAS oncogene (rs61764370) which is associated with cancer. We aimed to investigate the association of this KRAS variant with breast cancer and tumour biology. Methods We assessed frequency distributions of the KRAS variant in 415 patients with histologically confirmed breast cancer and 457 controls from Connecticut, USA (study group 1) and association of this variant with breast-cancer subtypes in 690 Irish women with known oestrogen receptor (ER), progesterone receptor (PR), and HER2 statuses, and 360 controls (study group 2). We pooled data for study groups 1 and 2 with a cohort of 140 women with triple-negative breast cancer and 113 controls to assess the association of the KRAS variant with triple-negative breast cancer risk, and genome-wide mRNA and specific miRNA expression in patients with triple-negative breast cancer. Findings Although frequency distributions of the KRAS variant in study group 1 did not differ between all genotyped individuals, eight (33%) of 24 premenopausal women with ER/PR-negative cancer had the KRAS variant, compared with 27 (13%) of 201 premenopausal controls (p=0.015). In study group 2, the KRAS variant was significantly enriched in women with triple-negative breast cancer (19 [21%] of 90 cases) compared with 64 (13%) of 478 for luminal A, 13 (15%) of 87 for luminal B, and two (6%) of 35 for HER2-positive subgroups (p=0.044). Multivariate analysis in the pooled study groups showed that the KRAS variant was associated with triple-negative breast cancer in premenopausal women (odds ratio 2.307, 95% CI 1.261-4.219, p=0.0067). Gene-expression analysis of triple-negative breast-cancer tumours suggested that KRAS-variant positive tumours have significantly altered gene expression, and are enriched for the luminal progenitor and BRCA1 deficiency signatures. miRNA analysis suggested reduced levels of let-7 miRNA species in KRAS-variant tumours. Interpretation The KRAS variant might be a genetic marker for development of triple-negative breast cancer in premenopausal women, and altered gene and miRNA expression signatures should enable molecular and biological stratification of patients with this subgroup of breast cancer

A 3′-untranslated region kras variant and triple-negative breast cancer: a case-control and genetic analysis

Background We previously identified a functional variant in a let-7 microRNA (miRNA) complementary site in the 3'-untranslated region of the KRAS oncogene (rs61764370) which is associated with cancer. We aimed to investigate the association of this KRAS variant with breast cancer and tumour biology. Methods We assessed frequency distributions of the KRAS variant in 415 patients with histologically confirmed breast cancer and 457 controls from Connecticut, USA (study group 1) and association of this variant with breast-cancer subtypes in 690 Irish women with known oestrogen receptor (ER), progesterone receptor (PR), and HER2 statuses, and 360 controls (study group 2). We pooled data for study groups 1 and 2 with a cohort of 140 women with triple-negative breast cancer and 113 controls to assess the association of the KRAS variant with triple-negative breast cancer risk, and genome-wide mRNA and specific miRNA expression in patients with triple-negative breast cancer. Findings Although frequency distributions of the KRAS variant in study group 1 did not differ between all genotyped individuals, eight (33%) of 24 premenopausal women with ER/PR-negative cancer had the KRAS variant, compared with 27 (13%) of 201 premenopausal controls (p=0.015). In study group 2, the KRAS variant was significantly enriched in women with triple-negative breast cancer (19 [21%] of 90 cases) compared with 64 (13%) of 478 for luminal A, 13 (15%) of 87 for luminal B, and two (6%) of 35 for HER2-positive subgroups (p=0.044). Multivariate analysis in the pooled study groups showed that the KRAS variant was associated with triple-negative breast cancer in premenopausal women (odds ratio 2.307, 95% CI 1.261-4.219, p=0.0067). Gene-expression analysis of triple-negative breast-cancer tumours suggested that KRAS-variant positive tumours have significantly altered gene expression, and are enriched for the luminal progenitor and BRCA1 deficiency signatures. miRNA analysis suggested reduced levels of let-7 miRNA species in KRAS-variant tumours. Interpretation The KRAS variant might be a genetic marker for development of triple-negative breast cancer in premenopausal women, and altered gene and miRNA expression signatures should enable molecular and biological stratification of patients with this subgroup of breast cancer