Viewing the immune checkpoint VISTA: landscape and outcomes across cancers.

BACKGROUND: Optimizing immune checkpoint inhibitor (ICI) therapy may require identification of co-targetable checkpoint pathways via immune profiling. Herein, we analyzed the transcriptomic expression and clinical correlates of V-domain immunoglobulin suppressor of T-cell activation (VISTA), a promising targetable checkpoint. PATIENTS AND METHODS: RNA sequencing was carried out on 514 tissues reflecting diverse advanced/metastatic cancers. Expression of eight immune checkpoint markers [lymphocyte-activation gene 3 (LAG-3), tumor necrosis factor receptor superfamily 14 (TNFRSF14), programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), programmed death-ligand 2 (PD-L2), B- and T-lymphocyte attenuator (BTLA), T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3), cytotoxic T-lymphocyte antigen 4 (CTLA-4)], in addition to VISTA, was analyzed, along with clinical outcomes. RESULTS: High VISTA RNA expression was observed in 32% of tumors (66/514) and was the most common highly expressed checkpoint among the nine assessed. High VISTA expression was independently correlated with high BTLA, TIM-3, and TNFRSF14, and with a diagnosis of pancreatic, small intestine, and stomach cancer. VISTA transcript levels did not correlate with overall survival (OS) from metastatic/advanced disease in the pan-cancer cohort or with immunotherapy outcome (progression-free survival and OS from the start of ICI) in 217 ICI-treated patients. However, in ICI-treated pancreatic cancer patients (n = 16), median OS was significantly shorter (from immunotherapy initiation) for the high- versus not-high-VISTA groups (0.28 versus 1.21 years) (P = 0.047); in contrast, VISTA levels were not correlated with OS in 36 pancreatic cancer patients who did not receive ICI. CONCLUSION: High VISTA expression correlates with high BTLA, TIM-3, and TNFRSF14 checkpoint-related molecules and with poorer post-immunotherapy survival in pancreatic cancer, consistent with prior literature indicating that VISTA is prominently expressed on CD68+ macrophages in pancreatic cancers and requiring validation in larger prospective studies. Immunomic analysis may be important for individualized precision immunotherapy.

Determining the Tsallis parameter via maximum entropy.

The nonextensive entropic measure proposed by Tsallis [C. Tsallis, J. Stat. Phys. 52, 479 (1988)] introduces a parameter, q, which is not defined but rather must be determined. The value of q is typically determined from a piece of data and then fixed over the range of interest. On the other hand, from a phenomenological viewpoint, there are instances in which q cannot be treated as a constant. We present two distinct approaches for determining q depending on the form of the equations of constraint for the particular system. In the first case the equations of constraint for the operator Ô can be written as Tr(F(q)Ô)=C, where C may be an explicit function of the distribution function F. We show that in this case one can solve an equivalent maxent problem which yields q as a function of the corresponding Lagrange multiplier. As an illustration the exact solution of the static generalized Fokker-Planck equation (GFPE) is obtained from maxent with the Tsallis enropy. As in the case where C is a constant, if q is treated as a variable within the maxent framework the entropic measure is maximized trivially for all values of q. Therefore q must be determined from existing data. In the second case an additional equation of constraint exists which cannot be brought into the above form. In this case the additional equation of constraint may be used to determine the fixed value of q.

Intrachromosomal genomic instability in human sporadic colorectal cancer measured by genome-wide allelotyping and inter-(simple sequence repeat) PCR.

We have used genome-wide allelotyping with 348 polymorphic autosomal markers spaced, on average, 10 cM apart to quantitate the extent of intrachromosomal instability in 59 human sporadic colorectal carcinomas. We have compared instability measured by this method with that measured by inter-(simple sequence repeat) PCR and microsatellite instability assays. Instability quantitated by fractional allelic loss rates was found to be independent of that detected by microsatellite instability analyses but was weakly associated with that measured by inter-(simple sequence repeat) PCR. A set of seven loci were identified that were most strongly associated with elevated rates of fractional allelic loss and/or inter-(simple sequence repeat) PCR instability; these seven loci were on chromosomes 3, 8, 11, 13, 14, 18, and 20. A lesser association was seen with two loci flanking p53 on chromosome 17. Coordinate loss patterns for these loci suggest that at least two separate sets of cooperating loci exist for intrachromosomal genomic instability in human colorectal cancer.

Associations between ERCC2 polymorphisms and gliomas.

Xeroderma pigmentosum complementation group D/excision repair cross-complementing in rodents 2 (ERCC2) encodes a protein that is part of the nucleotide excision repair pathway and the transcription factor IIH transcription complex. Mutations in this gene have been shown to cause three distinct clinical diseases including xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. Several ERCC2 polymorphisms, the effects of which on gene function are not known, have been described. To investigate whether constitutive sequence variations might be associated with adult onset gliomas, blood specimens from a case-control study (187 cases and 169 controls) were genotyped for seven previously described polymorphisms (R156R, I199M, H201Y, D312N, A575A, D711D, and K751Q). A novel R616C polymorphism was also identified. Cases were significantly more likely than controls to be homozygous for the silent AA variant at codon 156 (odds ratio, 2.3; 95% confidence interval, 1.3-4.2). Although this was observed for patients in each of three histological subgroups of cases, (glioblastoma multiforme, astrocytoma, and oligoastrocytoma) compared with controls, the association was strongest for patients with oligoastrocytoma (odds ratio, 3.2; 95% confidence interval, 1.1-9.5). In contrast, cases were somewhat less likely than controls to carry variants at D312N, D711D, and K751Q, but not significantly so overall or for any subgroup after adjustment for age and gender. Individuals with variant nucleotides at D312N, D711D, and K751Q were significantly more likely to carry a variant at another of those three codons and less likely to carry a variant nucleotide at R156R, regardless of case or control status. Although the pattern of association observed here is consistent with a role of ERCC2 variants in the prevention or causation of glioma, these results are also consistent with the possibility that another gene linked to ERCC2 may be involved. This seems especially so because the strongest association was observed with a silent nucleotide variation.

Semiautomated clone verification by real-time PCR using molecular beacons.

Conventional, high-throughput PCR analysis of common elements utilizing numerous primer sets and template DNA requires multiple rounds of PCR to ensure optimal conditions. Laborious gel electrophoresis and staining is then necessary to visualize amplification products. We propose novel multicolor molecular beacons, to establish a high-throughput, PCR-based sequence tagged site (STS) detection system that swiftly and accurately confirms marker content in template containing common repeat elements. A simple, one-tube, real-time PCR assay system was developed to specifically detect regions containing CA and GATA repeats. Ninety-six samples can be confirmed for marker content in a closed-tube format in 3 h, eliminating product confirmation on agarose gels and avoiding crossover contamination. Multiple STSs can be detected simultaneously in the same reaction tube by utilizing molecular beacons labeled with multicolor fluorophores. Template DNA from 260 RPCI-11 bacterial artificial chromosome (BAC) clones was examined for the presence of CA and/or GATA repeats using molecular beacon PCR and compared with conventional PCR results of the same clones. Of the 205 clones containing CA and GATA repeats, we were able to identify 129 clones (CA, n = 99; GATA, n = 30) by using molecular beacons and only 121 clones (CA, n = 92; GATA, n = 29) by conventional PCR amplification. As anticipated, 55 clones that contained sequences other than CA or GATA failed molecular beacon detection. Molecular beacon PCR, employing beacons specific for tandem repeat elements, provides a fast, accurate, and sensitive multiplex detection assay that will expedite verification of marker content in a multitude of template containing these repeats.

Chromosome identification using hidden Markov models: comparison with neural networks, singular value decomposition, principal components analysis, and Fisher discriminant analysis.

The analysis of G-banded chromosomes remains the most important tool available to the clinical cytogeneticist. The analysis is laborious when performed manually, and the utility of automated chromosome identification algorithms has been limited by the fact that classification accuracy of these methods seldom exceeds about 80% in routine practice. In this study, we use four new approaches to automated chromosome identification--singular value decomposition (SVD), principal components analysis (PCA), Fisher discriminant analysis (FDA), and hidden Markov models (HMM)--to classify three well-known chromosome data sets (Philadelphia, Edinburgh, and Copenhagen), comparing these approaches with the use of neural networks (NN). We show that the HMM is a particularly robust approach to identification that attains classification accuracies of up to 97% for normal chromosomes and retains classification accuracies of up to 95% when chromosome telomeres are truncated or small portions of the chromosome are inverted. This represents a substantial improvement of the classification accuracy for normal chromosomes, and a doubling in classification accuracy for truncated chromosomes and those with inversions, as compared with NN-based methods. HMMs thus appear to be a promising approach for the automated identification of both normal and abnormal G-banded chromosomes.

Molecular and cytogenetic analysis of familial Xp deletions.

Five families in which an Xp deletion is segregating and two families in which an X chromosome rearrangement including a deletion of the short arm is segregating were ascertained for study. Normal fertility was seen in all families. Members from 5 of the 7 families manifested short stature (height <5th centile), while normal height was present in two families. Studies of both the FMR-1 and the androgen receptor loci using PCR based X-inactivation analysis demonstrated that in all families analyzed, there is preferential inactivation of one X chromosome. Molecular cytogenetic analysis showed that members of 3 of the 7 families share a common breakpoint in an approximate 2-3 Mb region at Xp22.12, suggesting a possible hotspot for chromatin breakage. Previous genotype-phenotype correlations and deletion mapping have indicated that a gene for stature resides within the pseudoautosomal region in Xp22.33. Our findings indicate that the loss of this region is not always associated with short stature, suggesting that other factors may be involved.

The allele frequency of mutations in four genes that confer enhanced susceptibility to venous thromboembolism in an unselected group of New York State newborns.

The frequencies of Factor V G1691A (FVL), prothrombin (PT) G20210A, 5'10'methylenetetrahydrofolate reductase (MTHFR) C677T, and methionine synthase (MS) A2756G (four mutations associated with an increased risk of venous thromboembolism [VTE]) were determined in a sample of approximately 1500 New York State residents. Dried blood spots from approximately equal numbers of Caucasians, African-Americans and Hispanics were anonymously obtained from the New York State Department of Health Newborn Screening Program. Following PCR amplification of dried blood spot DNA, allele-specific oligonucleotide hybridization was used to detect mutant alleles. The total number of individuals at increased genetic risk for VTE was 271 (17.5%) of the 1553 persons tested. Increased genetic risk was defined as the heterozygous state for FVL or PT and the homozygous state for the MTHFR or MS polymorphisms. Sixteen individuals had more than one genetic risk factor. The MS gene variant allele frequencies for African-Americans and Hispanics are the first to be reported. This report also provides an estimate of the variant PT allele in the largest group of Hispanics studied to date.

Anesthesia for electroconvulsive therapy: a review.

Anesthetic techniques have evolved to improve the comfort and safety of modern electroconvulsive therapy (ECT). The authors review the literature and discuss the selection, preparation, and management from an anesthetic perspective. Specifically, the management of medications preprocedure and coexisting diseases is discussed. A review of induction agents, muscle relaxants, and other medications utilized in ECT is included.

Chromosome breakage hotspots and delineation of the critical region for the 9p-deletion syndrome.

The clinical features of the 9p-deletion syndrome include dysmorphic facial features (trigonocephaly, midface hypoplasia, upward-slanting palpebral fissures, and a long philtrum) and mental retardation. The majority of these patients appear to have similar cytogenetic breakpoints in 9p22, but some cases show phenotypic heterogeneity. To define the breakpoints of the deleted chromosomes, we studied 24 patients with a deletion of 9p, by high-resolution cytogenetics, FISH with 19 YACs, and PCR using 25 different sequence-tagged sites. Of 10 different breakpoints identified, 9 were localized within an approximately 5-Mb region, in 9p22-p23, that encompasses the interval between D9S1869 (telomeric) and D9S162 (centromeric). Eight unrelated patients had a breakpoint (group 1) in the same interval, between D9S274 (948h1) and D9S285 (767f2), suggesting a chromosome-breakage hotspot. Among 12 patients, seven different breakpoints (groups 3-9) were localized to a 2-Mb genomic region between D9S1709 and D9S162, which identified a breakpoint-cluster region. The critical region for the 9p-deletion syndrome maps to a 4-6-Mb region in 9p22-p23. The results from this study have provided insight into both the heterogeneous nature of the breakage in this deletion syndrome and the resultant phenotype-karyotype correlations.

Population-based studies reveal differences in the allelic frequencies of two functionally significant human interleukin-4 receptor polymorphisms in several ethnic groups.

PURPOSE: The presence of functionally significant human interleukin-4 receptor sequence variants, Gln551Arg and Ile50Val, was examined in four anonymous New York State populations defined by ethnic origin. These variants were studied because they are associated with atopy or atopic asthma whose prevalence varies in different populations. METHODS: PCR/RFLP (Ile50Val) and PCR/allele-specific oligonucleotide hybridization (Gln551Arg) assays were developed to detect both polymorphisms in 855 newborn screening specimens. RESULTS: Arg551 was most frequently found in Blacks (allele frequency of 68%). However, the Ile50 allele was most common in Whites (allele frequency, 87%). Significantly more Blacks had chromosomes bearing both of the "enhanced signaling" variants (Ile50/Arg551). CONCLUSIONS: Enhanced IL-4R signaling is associated with increased IgE production (atopy). Therefore, our data suggest that the African American population may be at increased risk for diseases, including asthma, which are associated with atopy. These data also emphasize the importance of determining the frequencies of single nucleotide polymorphisms in different populations before drawing conclusions from allele association studies, since the background allele frequencies may be disparate between different populations.

Rapid, efficient method for multiplex amplification from filter paper.

Guthrie cards derived from the New York State Newborn Screening Program were utilized to develop a rapid, economical method for amplifying multiple genes to detect mutations that impact public health. These specimens are untraceable to the donor because identifiers are removed and discarded; therefore, these pilot studies were carried out anonymously. The sample preparation requires minimal manipulation, is amenable to automation, and is useful in laboratories which routinely process large numbers of samples, such as those in typical newborn screening laboratories. Multiple gene fragments may be amplified from a 1 mm punch which contains less than 1 microl of whole blood. The blood spots used in these studies contain sufficient material for up to 25 amplification reactions which multiplex at least four different gene fragments each. Since sufficient material remains on the card after the routine testing is complete, this simple assay can greatly expand the efficacy of current newborn screening programs by permitting DNA diagnosis of some disorders when indicated, particularly those in which genotype-phenotype correlations are useful. In addition to newborn screening specimens, this method is also applicable to whole blood from adults after phlebotomy and from lymphoblastoid cell lines. Use of filter paper for DNA analysis is particularly useful for shipped specimens or for population studies whose subjects are refractory to phlebotomy.

The anesthetic management of the pediatric strabismus patient.

Postoperative nausea and vomiting continues to be a common perioperative complication for pediatric strabismus patients. Postoperative pain management and the choice of general anesthetic can increase the incidence of perioperative nausea. Current techniques for induction of general anesthesia and selection of agents, prevention and treatment of postoperative pain, and options for antiemetic therapy will be reviewed.

Balanced translocation 46,XY,t(2;15)(q37.2;q11.2) associated with atypical Prader-Willi syndrome.

The lack of normally active paternal genes in 15q11-q13, as an outcome of either a paternal deletion or maternal disomy, accounts for >95% of all patients with Prader-Willi syndrome. Other mechanisms, including imprinting mutations and unbalanced translocations involving pat 15q11-q13, have been described elsewhere. In this study, we present a patient with a rare balanced, de novo translocation-46,XY,t(2;15)(q37.2;q11.2)-involving breakage within the Prader-Willi/Angelman syndrome region of the paternal homologue, without an apparent deletion. The patient demonstrated several manifestations of the Prader-Willi syndrome but was clinically atypical. Cytogenetic and molecular studies of this case demonstrated the translocation breakpoint to be between SNRPN and IPW, with mRNA expression of SNRPN and PAR-5 but absence of IPW and PAR-1 expression. These results suggest that disruption of either IPW expression or a nearby gene by an upstream break may contribute to the Prader-Willi syndrome phenotype and that expression of SNRPN or other upstream genes is responsible for other aspects of the classical Prader-Willi syndrome phenotype.

Vertical transmission of HIV in New York State: a basis for statewide testing of newborns.

Infants (n = 313) of HIV-infected mothers were enrolled (mean age 1.9 weeks, range 0-8 weeks) in a 3-year prospective study of vertical transmission. Fifty-six infants (17.9%) had laboratory and clinical evidence of HIV infection. Polymerase chain reaction (PCR) provided early and reliable identification of infected infants. Thirty-one of the 56 infected infants had specimens submitted when the infants were 4 weeks of age or less and 30 (97%) tested PCR positive. This percentage increased to 100% by 8 weeks of age when 51 of the 56 infected infants had specimens tested for that time period. Immune complex dissociation (ICD) antigen testing was a sensitive method for diagnosis of infection but only in infants older than 1 month. p24 antigen testing, although free of false positives, is less sensitive than either of the other methods. Among surrogate markers of HIV infection, elevation of soluble CD8 levels precedes an increase in immunoglobulin levels or a decline in CD4 T lymphocytes. Vertical transmission is significantly lower in Central and Western New York State than other regions. Transmission is significantly higher in low birthweight babies and in infants whose mothers have CD4 counts < 500. This study provided the basis for establishing a Pediatric HIV PCR Testing Service for the early diagnosis of HIV infection in neonates.

Clinical spectrum and molecular diagnosis of Angelman and Prader-Willi syndrome patients with an imprinting mutation.

Recent studies have identified a new class of Prader-Willi syndrome (PWS) and Angelman syndrome (AS) patients who have biparental inheritance, but neither the typical deletion nor uniparental disomy (UPD) or translocation. However, these patients have uniparental DNA methylation throughout 15q11-q13, and thus appear to have a mutation in the imprinting process for this region. Here we describe detailed clinical findings of five AS imprinting mutation patients (three families) and two PWS imprinting mutation patients (one new family). All these patients have essentially the classical clinical phenotype for the respective syndrome, except that the incidence of microcephaly is lower in imprinting mutation AS patients than in deletion AS patients. Furthermore, imprinting mutation AS and PWS patients do not typically have hypopigmentation, which is commonly found in patients with the usual large deletion. Molecular diagnosis of these cases is initially achieved by DNA methylation analyses of the DN34/ZNF127, PW71 (D15S63), and SNRPN loci. The latter two probes have clear advantages in the simple molecular diagnostic analysis of PWS and AS patients with an imprinting mutation, as has been found for typical deletion or UPD PWS and AS cases. With the recent finding of inherited microdeletions in PWS and AS imprinting mutation families, our studies define a new class of these two syndromes. The clinical and molecular identification of these PWS and AS patients has important genetic counseling consequences.

Cytogenetic and molecular genetic characterization of trisomy 20 mosaicism in fetal blood and tissues.

We report a case of mosaic trisomy 20, the most common autosomal mosaicism identified in amniocytes, ascertained in a woman referred for amniocentesis because of abnormal ultrasound at 18.1 weeks' gestation which revealed short femurs and nuchal thickening. Metaphase analysis of 98 clones revealed 47,XY, +20 in 96 cells (98 per cent). Trisomy 20 was demonstrated in 6 cells (12 per cent) in a total of 50 cells from two fetal blood cultures obtained after pregnancy termination. Fluorescence in situ hybridization (FISH) analysis of interphase nuclei utilizing a chromosome 20 alpha-satellite centromeric DNA probe revealed three signals in 57/546 nuclei (10 per cent) in fetal blood. Metaphase analysis of 167 cells from seven different fetal tissue sources revealed trisomy 20 in 32 cells (19.2 per cent). The percentage of trisomy 20 cells varied with tissue type, with the highest percentage (13/25 cells, 52 per cent) identified in the small intestine and lymph nodes and the lowest percentage (1/34 cells, 2.9 per cent) identified in a specimen of chorionic villi. Molecular genetic analyses utilizing polymerase chain reaction (PCR)-formated dinucleotide repeat polymorphisms demonstrated that the non-disjunctional event most likely occurred post-zygotically and that the origin of the extra chromosome 20 was maternal. This study is the first to demonstrate trisomy 20 cells in fetal blood, suggesting that mosaic trisomy 20 can be embryonic in origin. In cases of prenatally detected mosaic trisomy 20, examination of fetal blood should be considered, as well as study of placental membranes, skin, and urine sediment to confirm the karyotype and determine its significance.

The effects of desmopressin and 6% hydroxyethyl starch on factor VIII:C.

In moderate doses of 20 mL/kg (1.2 g/kg), hydroxyethyl starch (HES) 6% decreases factor VIII:C activity. Desmopressin (DDAVP) increases circulating levels of factor VIII:C by stimulating the release of factor VIII:C from peripheral storage sites. The objective of this study was to monitor the changes in factor VIII:C associated with sequential HES and DDAVP administration. Thirty patients undergoing surgical procedures with a predicted blood loss of less than 750 mL were enrolled. After induction of anesthesia, HES was administered, 20 mL/kg, to a maximum of 1500 mL, at a rate to meet intraoperative fluid requirements. Patients then randomly received either a 10-mL solution containing 0.3 microgram/kg of DDAVP (Group 1) or 10 mL of normal saline (Group 2). After HES administration, factor VIII:C levels decreased significantly, to 69% of baseline, in both groups. After study drug administration, factor VIII:C in Group 1 increased significantly to 135% of baseline at 30 min and 115% of baseline at 60 min while in Group 2 average factor VIII:C levels remained below baseline at 30 and 60 min. DDAVP produced an increase in factor VIII:C activity despite HES administration and should be considered a treatment option for the mild coagulopathy infrequently associated with HES administration.

Management of cancer pain.

Pain is often the first symptom of cancer. Pain and fear of pain are concerns of most cancer patients and their families. The therapeutic options available to control pain are numerous, allowing practitioners to better individualize treatment. We present an overview of the pathophysiology of cancer pain, the current theories of pharmacologic opioid management, advantages of adjuvant drugs, and the range of invasive and noninvasive procedures that practitioners can offer their patients who have cancer-related pain.