KEAP1-driven co-mutations in lung adenocarcinoma unresponsive to immunotherapy despite high tumor mutational burden.

BACKGROUND: Immune checkpoint inhibitors (ICIs) have demonstrated significant overall survival (OS) benefit in lung adenocarcinoma (LUAD). Nevertheless, a remarkable interpatient heterogeneity characterizes immunotherapy efficacy, regardless of programmed death-ligand 1 (PD-L1) expression and tumor mutational burden (TMB). KEAP1 mutations are associated with shorter survival in LUAD patients receiving chemotherapy. We hypothesized that the pattern of KEAP1 co-mutations and mutual exclusivity may identify LUAD patients unresponsive to immunotherapy. PATIENTS AND METHODS: KEAP1 mutational co-occurrences and somatic interactions were studied in the whole MSKCC LUAD dataset. The impact of coexisting alterations on survival outcomes in ICI-treated LUAD patients was verified in the randomized phase II/III POPLAR/OAK trials (blood-based sequencing, bNGS cohort, N = 253). Three tissue-based sequencing studies (Rome, MSKCC and DFCI) were used for independent validation (tNGS cohort, N = 289). Immunogenomic features were analyzed using The Cancer Genome Atlas (TCGA) LUAD study. RESULTS: On the basis of KEAP1 mutational co-occurrences, we identified four genes potentially associated with reduced efficacy of immunotherapy (KEAP1, PBRM1, SMARCA4 and STK11). Independent of the nature of co-occurring alterations, tumors with coexisting mutations (CoMut) had inferior survival as compared with single-mutant (SM) and wild-type (WT) tumors (bNGS cohort: CoMut versus SM log-rank P = 0.048, CoMut versus WT log-rank P < 0.001; tNGS cohort: CoMut versus SM log-rank P = 0.037, CoMut versus WT log-rank P = 0.006). The CoMut subset harbored higher TMB than the WT disease and the adverse significance of coexisting alterations was maintained in LUAD with high TMB. Significant immunogenomic differences were observed between the CoMut and WT groups in terms of core immune signatures, T-cell receptor repertoire, T helper cell signatures and immunomodulatory genes. CONCLUSIONS: This study indicates that coexisting alterations in a limited set of genes characterize a subset of LUAD unresponsive to immunotherapy and with high TMB. An immune-cold microenvironment may account for the clinical course of the disease.

KRAS G12C mutation and risk of disease recurrence in stage I surgically resected lung adenocarcinoma.

KRAS G12C mutations are found in about 12-13% of LUAD samples and it is unclear whether they are associated with worse survival outcomes in resected, stage I LUAD. We assessed whether KRAS-G12C mutated tumours had worse DFS when compared to KRAS-nonG12C mutated tumours and to KRAS wild-type tumours in a cohort of resected, stage I LUAD (IRE cohort). We then leveraged on publicly available datasets (TCGA-LUAD, MSK-LUAD604) to further test the hypothesis in external cohorts. In the stage I IRE cohort we found a significant association between the KRAS-G12C mutation and worse DFS in multivariable analysis (HR: 2.47). In the TCGA-LUAD stage I cohort we did not find statistically significant associations between the KRAS-G12C mutation and DFS. In the MSK-LUAD604 stage I cohort we found that KRAS-G12C mutated tumours had worse RFS when compared to KRAS-nonG12C mutated tumours in univariable analysis (HR 3.5). In the pooled stage I cohort we found that KRAS-G12C mutated tumours had worse DFS when compared to KRAS-nonG12C mutated tumours (HR 2.6), to KRAS wild-type tumours (HR 1.6) and to any other tumours (HR 1.8); in multivariable analysis, the KRAS-G12C mutation was associated with worse DFS (HR 1.61). Our results suggest that patients with resected, stage I LUAD with a KRAS-G12C mutation may have inferior survival outcomes..

MicroRNA-based signatures impacting clinical course and biology of ovarian cancer: a miRNOmics study.

BACKGROUND: In Western countries, ovarian cancer (OC) still represents the leading cause of gynecological cancer-related deaths, despite the remarkable gains in therapeutical options. Novel biomarkers of early diagnosis, prognosis definition and prediction of treatment outcomes are of pivotal importance. Prior studies have shown the potentials of micro-ribonucleic acids (miRNAs) as biomarkers for OC and other cancers. METHODS: We focused on the prognostic and/or predictive potential of miRNAs in OC by conducting a comprehensive array profiling of miRNA expression levels in ovarian tissue samples from 17 non-neoplastic controls, and 60 tumor samples from OC patients treated at the Regina Elena National Cancer Institute (IRE). A set of 54 miRNAs with differential expression in tumor versus normal samples (T/N-deregulated) was identified in the IRE cohort and validated against data from the Cancer Genoma Atlas (TCGA) related to 563 OC patients and 8 non-neoplastic controls. The prognostic/predictive role of the selected 54 biomarkers was tested in reference to survival endpoints and platinum resistance (P-res). RESULTS: In the IRE cohort, downregulation of the 2 miRNA-signature including miR-99a-5p and miR-320a held a negative prognostic relevance, while upregulation of miR-224-5p was predictive of less favorable event free survival (EFS) and P-res. Data from the TCGA showed that downregulation of 5 miRNAs, i.e., miR-150, miR-30d, miR-342, miR-424, and miR-502, was associated with more favorable EFS and overall survival outcomes, while miR-200a upregulation was predictive of P-res. The 9 miRNAs globally identified were all included into a single biologic signature, which was tested in enrichment analysis using predicted/validated miRNA target genes, followed by network representation of the miRNA-mRNA interactions. CONCLUSIONS: Specific dysregulated microRNA sets in tumor tissue showed predictive/prognostic value in OC, and resulted in a promising biological signature for this disease.

Novel lectin-related proteins are major components in lima bean (Phaseolus lunatus L.) seeds.

The only component of the lectin-related protein family so far reported in Lima bean (Phaseolus lunatus L.) seeds is the minor seed lectin (LBL). In the morphotype Big Lima, we have isolated and characterised two abundant lectin-related seed proteins and the corresponding cDNA clones. The clones show 93.7% nucleotide identity and encode an arcelin-like (ARL) and an alpha-amylase inhibitor-like (AIL) protein. Not considering the signal peptides, ARL and AIL polypeptides contain 239 and 233 amino acids, respectively. Each polypeptide is present in the mature protein as two glycoforms. ARL subunits (43 and 46 kDa) make up oligomers of about 125 to 130 kDa whereas AIL subunits (40 and 42 kDa) oligomerise in dimers of about 88 to 100 kDa. cDNA clones encoding two isoforms of the less abundant Lima bean lectin were also isolated. In common bean (P. vulgaris) the lectin locus encodes the lectin and the lectin-related proteins alpha-amylase inhibitor and arcelin, all plant defence proteins. Our data indicate extensive evolution of the locus also in Lima bean.

Current smoking, occupation, N-acetyltransferase-2 and bladder cancer: a pooled analysis of genotype-based studies.

The aim of this study was to investigate the association of NAT2 gene polymorphism with bladder cancer using the data derived from the International Project on Genetic Susceptibility to Environmental Carcinogens. Four case control studies conducted in four European countries, plus two case series, one from England and one from Germany, for a total of 1530 cases and 731 controls (all Caucasian) were included. The interaction between NAT2 and bladder cancer considering smoking habits and occupational exposure was studied. There was a significant association between NAT2 and bladder cancer (odds ratio: 1.42, 95% confidence interval: 1.14-1.77), with a slightly significant heterogeneity among studies. However, heterogeneity disappeared when smokers were divided into current and ex-smokers. The risk of cancer was elevated in smokers and occupationally exposed subjects, with the highest risk among slow acetylators. The increase in risk was limited, in fact, to current smokers (odds ratio = 1.74, 95% confidence interval: 0.96-3.15). This analysis confirms that the NAT2 genotype is a risk factor for bladder cancer by interacting with smoking or occupational exposures. Our observation suggests that NAT2 is not a risk factors per se but modulates the effect of carcinogens contained in tobacco smoke (probably arylamines) or associated with occupational exposures.

Acrocallosal syndrome: a new case.

We describe a 2-month-old infant girl with typical clinical manifestations of the acrocallosal syndrome: characteristic face, agenesis of corpus callosum, polydactyly associated with other anomalies of the extremities, and mental retardation. The importance of a correct nosology and genetic counseling is underlined on the basis of the description of familiar cases of the syndrome.

Multiple congenital anomalies associated with apparently normal maternal intake of vitamin A: a phenocopy of the isotretinoin syndrome?

The teratogenicity of vitamin A has been repeatedly reported in the literature and confirmed on the basis of several cases of adverse pregnancy outcome associated with maternal isotretinoin exposure. We report a case which shows a striking similarity with this syndrome, but the child was born to a mother who took a normal supplementation of vitamin A during pregnancy. The differential diagnosis is discussed.

Assessment of adrenal gland volume by computed tomography in depressed patients and healthy volunteers: a pilot study.

Excessive adrenocortical activation in depression has been postulated to be the result of overactivity of limbic system-hypothalamic function. In contrast, several studies have suggested the possibility that excessive secretion of cortisol might also result, in part, from a heightened adrenocortical responsiveness to adrenocorticotropic hormone (ACTH), or even a mild adrenal hyperplasia. Because computed tomography (CT) may provide a method for assessing an increase in adrenal size, we performed CT scans of the adrenal glands in depressed patients and healthy volunteers, who also received the dexamethasone suppression test. Eight out of 16 patients (50%) had adrenal volumes in excess of the 95th percentile value of the control distribution for adrenal volume. These observations suggest that there may be demonstrable adrenal hypertrophy during depressive illness.

International collaborative study on genetic susceptibility to environmental carcinogens (GSEC): an update.

We have created a database of published and unpublished studies on genetic susceptibility to environmental carcinogens, by bringing together many single studies that are too small to give definitive answers on the role of metabolic genes in cancer susceptibility. Possible participants were identified through a literature search of case control studies published up to June 1999 on metabolic gene polymorphisms and cancer, and invited to send their data sets without personal identifiers. Individual data from a total of over 30,000 subjects (52% cancer cases, 48% controls) have been collected. The most common type of cancer is lung, followed by bladder, head and neck, and breast. Demographic data, such as age, sex, and race were obtained for almost all the subjects. Main exposures, such as smoking, alcohol, occupational exposure were also included in a portion of the data set. The simultaneous presence of two gene polymorphisms has been assessed in 3535 controls and 3445 cases. An Advisory Committee has evaluated and approved 8 proposals to analyze the available data. This project allows the study of the main effects of genes, gene-exposure effects, ethnic and geographic differences in allele frequencies, gene-environment and gene-gene interaction as possible risk factors for cancer.

Cost analysis of neodymium-YAG laser versus transurethral resection treatment of superficial bladder carcinoma.

We have analyzed a group of patients treated by various urologists with both neodymium-YAG laser photoirradiation and transurethral resection in the treatment of superficial bladder carcinoma. The average hospitalization for the group of patients treated by the laser was significantly shorter than the group of patients treated by transurethral resection of the bladder tumor. The complications were similar. The cost savings to patients treated by laser photoirradiation appears to be significantly greater in laser groups of patients as opposed to conventional transurethral resection techniques.

Absorption and excretion of dilute gastrografin during computed tomography in pseudomembranous colitis.

Since 1955, urinary tract opacification secondary to absorption of orally or rectally administered iodinated contrast material has been recognized. Previously reported cases have involved relatively large volumes of full strength contrast necessary for fluoroscopic examination of the gastrointestinal tract. Our purpose is to report a case of urinary tract opacification in a patient who received a small amount of oral contrast in a dilute solution as preparation for computed tomography examination.

Transcatheter biopsy of lesions obstructing the bile ducts.

A method was developed for biopsy sampling of masses obstructing the biliary system in patients with a biliary drainage catheter. The biopsy needle is inserted through the drainage catheter, with fluoroscopic guidance, to the site of the lesion. The technique has been used without complication in more than 30 patients with cancer of the pancreas and bile ducts.

Peripheral arterial Doppler ultrasonography: diagnostic criteria.

Fifty-one patients (86 legs) were studied from the aorta to the popliteal artery with both duplex ultrasonography and arteriography with the intention of establishing diagnostic ultrasonographic criteria for degrees of stenosis greater than 50% and determining the effect of multi-segment disease on the accuracy of these criteria. Receiver operator characteristic curves were used to determine diagnostic criteria for greater than 50%, greater than 70%, greater than 90% diameter stenoses or occlusions. A stenosis of greater than 70% was diagnosed either if the peak systolic velocity was more than 160 cm/sec (sensitivity 77%, specificity 90%) of if there was an increase in peak systolic velocity of 100% with respect to the arterial segment above the stenosis (sensitivity 80%, specificity 93%). Sequential stenoses were detected with lesser sensitivities. Ratio criteria were more accurate than peak systolic velocity for all degrees of stenosis. For detection of occlusion, duplex ultrasonography was 92% sensitive and 99% specific.

Diagnostic criteria for carotid duplex sonography.

Optimal criteria for the duplex sonographic diagnosis of carotid artery stenosis have not yet been defined. We studied 205 vessels in 105 patients with both duplex sonography and angiography. Four diagnostic groups were defined on the basis of Doppler flow characteristics. Receiver-operating-characteristic curves were used to compare diagnostic criteria at significant stenosis levels, and to select threshold values that emphasize specificity as well as sensitivity. Peak systolic velocity, systolic velocity ratios, and end-diastolic velocity were all shown to be equivalent predictors of significant disease. We chose peak systolic velocity in the internal carotid artery as our best parameter because of its ease of measurement. The use of combined parameters offered no significant statistical advantage over the use of a single parameter. The real-time assessment of stenosis and ulceration was not found to be reliable. ROC curves should be used to select Doppler criteria with desired sensitivities and specificities to maximize the benefit in each clinical setting.

Evaluation of the peripheral arteries with duplex US after angioplasty.

Duplex ultrasound (US) was performed in 22 patients before and immediately after percutaneous transluminal balloon angioplasty (PTA) for peripheral artery stenoses or occlusions. Two patients underwent PTA on two occasions, and one patient underwent PTA of each lower extremity, resulting in 25 duplex US imaging pairs at a total of 40 PTA sites. The criterion for significant stenosis on duplex US studies was an increase in peak systolic velocity of at least 100% compared with the velocity in the arterial segment proximal to the lesion (velocity ratio, greater than or equal to 2.0). For 22 paired duplex US studies, pulse volume recordings or ankle-brachial indexes were obtained before and after PTA. After PTA, eight patients had residual high velocity ratios at 12 PTA sites. Only two of these patients had a residual hemodynamic stenosis as determined with post-PTA arteriography, pulse volume recordings, or ankle-brachial indexes. In this study, duplex US that was performed immediately after PTA for evaluation of residual stenosis was frequently misleading.

The value of duplex sonography after peripheral artery angioplasty in predicting subacute restenosis.

OBJECTIVE: The purpose of this study was to determine if abnormal findings on duplex sonographic examination after peripheral artery angioplasty correlate with the subsequent recurrence of a stenosis. SUBJECTS AND METHODS: We used duplex sonography to examine 35 stenoses in 23 patients within 48 hr after the patients had angioplasty to treat these stenoses. Patients were followed up for 3 years by using one or more of the following: assessment of signs and symptoms, monitoring of peripheral pulses, pulse volume recordings, and angiography. Life tables were constructed to compare long-term patency with the presence of abnormal findings seen on duplex sonograms. Abnormal findings at the dilated segment included a blood-flow velocity greater than 120 cm/sec or a residual elevated velocity ratio greater than 1.4 or 2.0 immediately after angioplasty. RESULTS: Twelve (34%) of 35 angioplasty sites showed recurrent stenosis before 36 months. Patency at 24 months was calculated for velocities less than 120 cm/sec vs velocities of 120 cm/sec or greater (41% vs 68%), for velocity ratios less than 1.4 vs ratios of 1.4 or greater (63% vs 57%), and for velocity ratios less than 2.0 vs ratios of 2.0 or greater (54% vs 74%). We found no significant difference in patency between those patients with normal findings and those with abnormal findings on duplex sonographic examination after angioplasty. CONCLUSION: Abnormal findings on duplex sonograms obtained immediately after peripheral angioplasty cannot be used to predict subacute restenosis.

Expanding spectrum of pulmonary disease caused by nontuberculous mycobacteria.

The clinical and radiographic features of 35 patients with nontuberculous mycobacterial (NTMB) pulmonary infections were reviewed. Radiographs of half the patients showed the pattern of cavitary upper-lobe infiltrates typical of reactivation tuberculosis; those of the other half had a radiographic pattern characterized by patchy, nodular infiltrates without an upper-lobe prevalence. Approximately half of the latter group showed multiple small cavities resembling those seen in bronchiectasis. These results suggest that studies in which the diagnosis of NTMB infection has been made primarily from sputum cultures may have been biased toward detecting cavitary disease. The spectrum of pulmonary disease caused by NTMB appears to be larger than previously appreciated. An enhanced awareness of alternate presentations of NTMB infections may result in earlier diagnosis.

Observer variation in the detection of osteopenia.

In order to determine observer variation in the detection of osteopenia, 15 pairs of lateral chest radiographs obtained within two weeks of each other were reviewed separately by two radiologists and one orthopedist on three separate occasions. Intra- and interobserver variations were calculated for each individual film and film pairs using Kappa values. The individual observers were not able to give consistent readings on the same film on different days (average Kappa = 0.54). When the additional factors of repeat films (average kappa = 0.47), or separate observers (average Kappa = 0.38) were analyzed, agreement was even worse. The identification of osteopenia from the lateral view of the thoracic spine is highly subjective and variable from film to film and observer to observer.