Clinical and molecular correlates of PD-L1 expression in patients with lung adenocarcinomas.

BACKGROUND: Programmed death-ligand 1 (PD-L1) expression is the only FDA-approved biomarker for immune checkpoint inhibitors (ICIs) in patients with lung adenocarcinoma, but sensitivity is modest. Understanding the impact of molecular phenotype, clinical characteristics, and tumor features on PD-L1 expression is largely unknown and may improve prediction of response to ICI. PATIENTS AND METHODS: We evaluated patients with lung adenocarcinoma for whom PD-L1 testing and targeted next-generation sequencing (using MSK-IMPACT) was performed on the same tissue sample. Clinical and molecular features were compared across PD-L1 subgroups to examine how molecular phenotype associated with tumor PD-L1 expression. In patients treated with anti-PD-(L)1 blockade, we assessed how these interactions impacted efficacy. RESULTS: A total of 1586 patients with lung adenocarcinoma had paired PD-L1 testing and targeted next-generation sequencing. PD-L1 negativity was more common in primary compared to metastatic samples (P < 0.001). The distribution of PD-L1 expression (lymph nodes enriched for PD-L1 high; bones predominantly PD-L1 negative) and predictiveness of PD-L1 expression on ICI response varied by organ. Mutations in KRAS, TP53, and MET significantly associated with PD-L1 high expression (each P < 0.001, Q < 0.001) and EGFR and STK11 mutations associated with PD-L1 negativity (P < 0.001, Q = 0.01; P = 0.001, Q < 0.001, respectively). WNT pathway alterations also associated with PD-L1 negativity (P = 0.005). EGFR and STK11 mutants abrogated the predictive value of PD-L1 expression on ICI response. CONCLUSION: PD-L1 expression and association with ICI response vary across tissue sample sites. Specific molecular features are associated with differential expression of PD-L1 and may impact the predictive capacity of PD-L1 for response to ICIs.

Poor survival after resection of early gastric cancer: extremes of survivorship analysis reveal distinct genomic profile.

A subset of patients with early gastric cancer demonstrate early recurrence and poor survival despite margin-negative resection. This study used an extremes-of-survivorship approach to identify an association between TP53 hotspot mutations co-occurring with loss of heterozygosity and unexpectedly poor survival in early gastric cancer. This distinct genomic profile may be a novel biomarker of poor survival in patients with completely resected early gastric cancer, and warrants large-scale validation. Promising, validation needed.

Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group.

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

Oncologist use and perception of large panel next-generation tumor sequencing.

BACKGROUND: Genomic profiling is increasingly incorporated into oncology research and the clinical care of cancer patients. We sought to determine physician perception and use of enterprise-scale clinical sequencing at our center, including whether testing changed management and the reasoning behind this decision-making. PATIENTS AND METHODS: All physicians who consented patients to MSK-IMPACT, a next-generation hybridization capture assay, in tumor types where molecular profiling is not routinely performed were asked to complete a questionnaire for each patient. Physician determination of genomic 'actionability' was compared to an expertly curated knowledgebase of somatic variants. Reported management decisions were compared to chart review. RESULTS: Responses were received from 146 physicians pertaining to 1932 patients diagnosed with 1 of 49 cancer types. Physicians indicated that sequencing altered management in 21% (331/1593) of patients in need of a treatment change. Among those in whom treatment was not altered, physicians indicated the presence of an actionable alteration in 55% (805/1474), however, only 45% (362/805) of these cases had a genomic variant annotated as actionable by expert curators. Further evaluation of these patients revealed that 66% (291/443) had a variant in a gene associated with biologic but not clinical evidence of actionability or a variant of unknown significance in a gene with at least one known actionable alteration. Of the cases annotated as actionable by experts, physicians identified an actionable alteration in 81% (362/445). In total, 13% (245/1932) of patients were enrolled to a genomically matched trial. CONCLUSION: Although physician and expert assessment differed, clinicians demonstrate substantial awareness of the genes associated with potential actionability and report using this knowledge to inform management in one in five patients. CLINICAL TRIAL NUMBER: NCT01775072.

Phase I dose escalation study of the PI3kinase pathway inhibitor BKM120 and the oral poly (ADP ribose) polymerase (PARP) inhibitor olaparib for the treatment of high-grade serous ovarian and breast cancer.

Background: Based upon preclinical synergy in murine models, we carried out a phase I trial to determine the maximum tolerated dose (MTD), toxicities, pharmacokinetics, and biomarkers of response for the combination of BKM120, a PI3K inhibitor, and olaparib, a PARP inhibitor. Patients and methods: Olaparib was administered twice daily (tablet formulation) and BKM120 daily on a 28-day cycle, both orally. A 3 + 3 dose-escalation design was employed with the primary objective of defining the combination MTD, and secondary objectives were to define toxicities, activity, and pharmacokinetic profiles. Eligibility included recurrent breast (BC) or ovarian cancer (OC); dose-expansion cohorts at the MTD were enrolled for each cancer. Results: In total, 69 of 70 patients enrolled received study treatment; one patient never received study treatment because of ineligibility. Twenty-four patients had BC; 46 patients had OC. Thirty-five patients had a germline BRCA mutation (gBRCAm). Two DLTs (grade 3 transaminitis and hyperglycemia) were observed at DL0 (BKM120 60 mg/olaparib and 100 mg b.i.d.). The MTD was determined to be BKM120 50 mg q.d. and olaparib 300 mg b.i.d. (DL8). Additional DLTs included grade 3 depression and transaminitis, occurring early in cycle 2 (DL7). Anticancer activity was observed in BC and OC and in gBRCAm and gBRCA wild-type (gBRCAwt) patients. Conclusions: BKM120 and olaparib can be co-administered, but the combination requires attenuation of the BKM120 dose. Clinical benefit was observed in both gBRCAm and gBRCAwt pts. Randomized phase II studies will be needed to further define the efficacy of PI3K/PARP-inhibitor combinations as compared with a PARP inhibitor alone.

Molecular characterization of Staphylococcus aureus from outpatients in the Caribbean reveals the presence of pandemic clones.

Staphylococcus aureus infections continue to pose a global public health problem. Frequently, this epidemic is driven by the successful spread of single S. aureus clones within a geographic region, but international travel has been recognized as a potential risk factor for S. aureus infections. To study the molecular epidemiology of S. aureus infections in the Caribbean, a major international tourist destination, we collected methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolates from community-onset infections in the Dominican Republic (n = 112) and Martinique (n = 143). Isolates were characterized by a combination of pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing (MLST) typing. In Martinique, MRSA infections (n = 56) were mainly caused by t304-ST8 strains (n = 44), whereas MSSA isolates were derived from genetically diverse backgrounds. Among MRSA strains (n = 22) from the Dominican Republic, ST5, ST30, and ST72 predominated, while ST30 t665-PVL+ (30/90) accounted for a substantial number of MSSA infections. Despite epidemiological differences in sample collections from both countries, a considerable number of MSSA infections (~10%) were caused by ST5 and ST398 isolates at each site. Further phylogenetic analysis suggests the presence of lineages shared by the two countries, followed by recent genetic diversification unique to each site. Our findings also imply the frequent import and exchange of international S. aureus strains in the Caribbean.

Successes and challenges of latent TB screening and treatment in a high-prevalence US region.

BACKGROUND: South Texas has higher TB disease incidence than much of the United States. We evaluated a multi-site South Texas interferon-gamma release assay (IGRA)-based testing and latent TB infection (LTBI) treatment program targeting high-risk populations.METHODS: Number of IGRA tests, test results, LTBI confirmation, and treatment outcomes were collected over 2.5 years. Sixteen semi-structured patient interviews and 10 site-based focus groups were conducted with providers, nurses, and administrators. Grounded theory identified themes associated with successful outcomes.RESULTS: Of 9,050 IGRA tests, 687 (8%) were positive; 340 (49%) confirmed as LTBI; 191 initiated LTBI treatment; and 130 (68% of initiators) completed treatment. Patient barriers to treatment completion included lack of knowledge, misconceptions, and treatment toxicities. Clinic staff concurred that toxicity was a barrier to treatment and requiring new processes with limited resources were implementation barriers.CONCLUSIONS: Over 9,000 patients were screened with a high prevalence of IGRA positivity, but confirming LTBI, initiating, and completing treatment were challenging. Qualitative evaluation supports low literacy patient education on LTBI and toxicities and expanded support for process implementation and provider training. These findings highlight challenges at all levels of the LTBI care cascade and provide patient, staff, and provider perspectives on implementation of these programs.

Protocol for the pilot quasi-experimental controlled trial of a gender-responsive implementation strategy with providers to improve HIV outcomes in Uganda.

BACKGROUND: Antiretroviral treatment (ART) is the most effective clinical intervention for reducing morbidity and mortality among persons living with HIV. However, in Uganda, there are disparities between men and women in viral load suppression and related HIV care engagement outcomes, which suggests problems with the implementation of ART. Gender norms are a known driver of HIV disparities in sub-Saharan Africa, and patient-provider relationships are a key factor in HIV care engagement; therefore, the role of gender norms is important to consider in interventions to achieve the equitable provision of treatment and the quality of ART counseling. METHODS: The overall research objective of this study is to pilot test an implementation strategy (i.e., methods to improve the implementation of an evidence-based intervention) to increase providers' capacity to provide gender-responsive treatment and counseling to men and women on HIV treatment in Uganda. Delivered to HIV providers, this group training adapts evidence-based strategies to reduce gender biases and increase skills to deliver gender-specific and transformative HIV counseling to patients. The implementation strategy will be piloted through a quasi-experimental controlled trial. Clinics will be randomly assigned to either the intervention or control conditions. The trial will assess feasibility and acceptability and explore barriers and facilitators to implementation and future adoption while gathering preliminary evidence on the implementation strategy's effectiveness by comparing changes in patient (N = 240) and provider (N = 80-140) outcomes across intervention and control clinics through 12-month follow-up. Quantitative data will be descriptively analyzed, qualitative data will be analyzed through thematic analysis, and these data will be mixed during the presentation and interpretation of results where appropriate. DISCUSSION: This pilot intervention trial will gather preliminary evidence on the acceptability, feasibility, and potential effect of a novel implementation strategy to improve men and women's HIV care engagement, with the potential to reduce gender disparities in HIV outcomes. TRIAL REGISTRATION: Clinicaltrials.gov NCT05178979 , retrospectively registered on January 5, 2022.

Drug use, sexual risk, and structural vulnerability among female sex workers in two urban centers of the Dominican Republic: The EPIC study.

BACKGROUND: Evidence in different countries suggest an association between sex work and drug use. In the Dominican Republic an estimated 60,000-100,000 women work in the sex industry. However, little is known about their drug use behaviors. OBJECTIVE: To characterize the burden of drug use and examine correlates of these behaviors among female sex workers in the Dominican Republic. METHODS: Data for this analysis comes from a cross-sectional study among key populations at risk for HIV. A community sample of female sex workers (N = 389) was recruited using passive and active recruitment strategies. Participants completed a behavioral survey between 2015 and 2016. Logistic regression models were constructed to examine predictors of drug use. RESULTS: Protective factors against marijuana and crack or cocaine use included being heterosexual, having a higher level of education, regular employment, and fewer male sexual partners. Increased odds of crack or cocaine use were associated with incarceration, having slept in a place not meant for human habitation in the last six months, and having ever lived in a batey (a community around a sugar mill where workers and their families live). Participants that used marijuana were generally younger, while those that used crack or cocaine were older. CONCLUSIONS: Our findings highlight characteristics of the social and economic environment that require further research to optimize prevention and care strategies for this population. Public health interventions are needed that address drug use, sexual risk-taking, and helping female sex workers and their families achieve a healthy life.

Exposure to SSRI-type antidepressants increases righting time in the marine snail Ilyanassa obsoleta.

Exposure to human antidepressants has been shown to disrupt locomotion and other foot-mediated mechanisms in aquatic snails. We tested the effect of three selective serotonin reuptake inhibitor (SSRI)- and one selective serotonin-norepinephrine reuptake inhibitor (SNRI)-type antidepressants on the righting response in the marine snail, Ilyanassa obsoleta. All four antidepressants (fluoxetine, sertraline, paroxetine, venlafaxine) significantly increased righting time compared with controls with an exposure time as short as 1 h. Dose responses were nonmonotonic with effects seen mainly at the lowest exposure concentrations and shortest duration. The lowest concentration to show an effect was 3.45 µg/L fluoxetine with a 2-h exposure period and is about 3.71 times higher than environmental concentrations. Our results highlight rapid disruption of another foot-mediated behavior in aquatic snails by SSRI-type antidepressants. We discuss these and other reported nonmonotonic dose responses caused by antidepressants in terms of the various possible physiological mechanisms of action in nontarget aquatic species.

Ras and RhoA suppress whereas RhoB enhances cytokine-induced transcription of nitric oxide synthase-2 in human normal liver AKN-1 cells and lung cancer A-549 cells.

While both nitric oxide synthase-2 (NOS-2) and low molecular weight GTPases, such as Ras and Rho, have been implicated in malignant transformation, the cross talk between these important proteins is ill understood. In this study we examined the ability of H-Ras, RhoA, RhoB and Rac1 to modulate cytokine-induced NOS2. In the normal human liver AKN-1 cell line and in the human non-small cell lung carcinoma cell line, A-549, the ability of the cytokines (INF-gamma, IL-1beta and TNF-alpha) to activate NOS-2 was blocked by activated L61-H-Ras whereas dominant negative N17-H-Ras enhanced NOS-2 activation. Consistent with this dominant negative Erk2 as well as a MEK inhibitor also enhanced cytokine activation of NOS-2. Furthermore, activated L63-RhoA blocked whereas activated V14-RhoB enhanced cytokine NOS-2 activation. Activated I115-Racl did not affect NOS-2 activation. These results demonstrate that the Ras/Erk and the Ras/RhoA pathways negatively regulate whereas RhoB enhances cytokine-induced NOS-2. This is the first demonstration that genes that promote malignant transformation such as Ras and RhoA inhibit, whereas genes with tumor suppressor activity such as RhoB enhance NOS2 induction.

Molecular regulation of the human inducible nitric oxide synthase (iNOS) gene.

In critically ill patients, the human inducible nitric oxide synthase (iNOS) gene is expressed in nearly every organ and has been shown to be associated with the refractory hypotension of septic and hemorrhagic shock. The molecular regulation of iNOS expression is complex and occurs at multiple sites in the gene expression pathway. Work in our laboratory has demonstrated that a combination of cytokines synergistically activate iNOS expression, which has resulted in the cloning of the first human iNOS gene from cytokine-stimulated hepatocytes. In addition, we have demonstrated that iNOS expression is transcriptionally regulated and that the functional promoter elements are located upstream of -4.7 kilobases (kb) within a unique enhancer region containing four functional nuclear factor kappa B elements. These results contrast markedly with the murine iNOS promoter, where only 1.0 kb of 5'-flanking sequence is required for lipopolysaccharide and cytokine responsiveness. Furthermore, numerous mechanisms have evolved to down-regulate iNOS expression. By elucidating these mechanisms, therapeutic strategies to govern iNOS expression may be developed.

Inhibition of cytokine-induced nitric oxide synthase expression by gene transfer of adenoviral I kappa B alpha.

BACKGROUND: Nitric oxide is overexpressed in nearly every organ during sepsis and it has profound biologic effects. Previously, we showed that maximal inducible nitric oxide synthase (iNOS) expression is up-regulated by a combination of cytokines and that this effect is mediated by the transcription factor NF-kappa B. Therefore the purpose of this study was to establish whether gene transfer of the inhibitory molecule I kappa B would result in the abrogation of cytokine-induced iNOS expression. METHODS: Cultured hepatocytes were infected with an adenoviral vector containing the I kappa B alpha gene (Ad5I kappa B) and after an 18-hour recovery period were stimulated with the cytokine mixture of tumor necrosis factor-alpha (500 U/mL) plus interleukin 1 beta (200 U/mL) plus interferon gamma (100 U/mL). RESULTS: As expected, cytokine mixture induced significant hepatocyte nitrite (NO2-) and iNOS messenger RNA production. Cells infected with the I kappa B alpha gene showed a dose-dependent decrease in NO2- and iNOS messenger RNA levels. Western blot analysis showed a marked decrease in iNOS protein levels in the presence of Ad5I kappa B alpha. Gel shift assays of nuclear extracts demonstrated that Ad5I kappa B alpha decreased the cytokine-induced DNA binding activity for NF kappa B. CONCLUSIONS: NF kappa B is an important regulator of cytokine-induced NO expression. These results identify a novel therapeutic approach where gene transfer of the inhibitory molecule I kappa B alpha can be used to down-regulate cytokine-induced iNOS expression as well as other NF kappa B-dependent genes that are up-regulated during the inflammatory response.

Nitric oxide down-regulates hepatocyte-inducible nitric oxide synthase gene expression.

BACKGROUND: The expression of inducible nitric oxide synthase (iNOS) contributes to the systemic manifestations of sepsis. OBJECTIVE: To determine whether nitric oxide (NO) can exert negative feedback regulation on iNOS gene expression. SETTING: Molecular biology research laboratory of the department of surgery. STUDY DESIGN: Isolated rat hepatocytes were cultured with a cytokine mix consisting of tumor necrosis factor alpha, interleukin 1 beta, and interferon gamma in the presence or absence of the NO donor S-nitroso-N-acetyl-D,L-penicillamine. MAIN OUTCOME MEASURES: Nitrite and nitrate (NO2- and NO3-) levels were assayed. Hepatocyte iNOS messenger RNA and protein levels were assessed. Electromobility shift assays were performed for NF-kappa B DNA binding activity. Finally, iNOS enzyme activity was determined using high-performance liquid chromatography. RESULTS: Cytokine mix-induced hepatocyte iNOS mRNA and protein production and the addition of the NO donor S-nitroso-N-acetyl-D,L-penicillamine markedly attenuated iNOS mRNA and protein levels. Gel shift assays of the nuclear extracts disclosed that decreased cytokine mix-induced DNA binding activity for NF-kappa B in a concentration-dependent manner. Finally, NO failed to significantly inhibit iNOS enzyme activity. CONCLUSIONS: These data indicate that NO down-regulates iNOS gene transcription, and that the effect is mediated in part by inhibiting NF-kappa B activity. These results identify a novel negative feedback mechanism whereby NO down-regulates iNOS gene expression, possibly to limit overproduction during the septic response.

The surgical anatomy of the popliteal artery.

The popliteal artery is a common recipient site for above or below knee bypass grafts. It is also frequently affected by penetrating and blunt trauma involving the lower extremity. Exposure of this artery is, therefore, often required in both emergent and elective vascular procedures. In close proximity to the artery, within the confines of the popliteal fossa, are the tibial nerve, common peroneal nerve, and the popliteal vein. An understanding of the normal anatomy and the important variations in the popliteal bifurcation patterns is essential. In this report, we have combined data from new cadaver dissections with prior anatomical data to describe the anatomy of the popliteal fossa and important vascular anomalies.

Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring (V600E)BRAF.

Identifying the spectrum of genetic alterations that cooperate with critical oncogenes to promote transformation provides a foundation for understanding the diversity of clinical phenotypes observed in human cancers. Here, we performed integrated analyses to identify genomic alterations that co-occur with oncogenic BRAF in melanoma and abrogate cellular dependence upon this oncogene. We identified concurrent mutational inactivation of the PTEN and RB1 tumor suppressors as a mechanism for loss of BRAF/MEK dependence in melanomas harboring (V600E)BRAF mutations. RB1 alterations were mutually exclusive with loss of p16(INK4A), suggesting that whereas p16(INK4A) and RB1 may have overlapping roles in preventing tumor formation, tumors with loss of RB1 exhibit diminished dependence upon BRAF signaling for cell proliferation. These findings provide a genetic basis for the heterogeneity of clinical outcomes in patients treated with targeted inhibitors of the mitogen-activated protein kinase pathway. Our results also suggest a need for comprehensive screening for RB1 and PTEN inactivation in patients treated with RAF and MEK-selective inhibitors to determine whether these alterations are associated with diminished clinical benefit in patients whose cancers harbor mutant BRAF.