Precision neoantigen discovery using large-scale immunopeptidomes and composite modeling of MHC peptide presentation

Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anti-cancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass-spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past two decades. However, improvement in the sensitivity and specificity of prediction algorithms is needed for clinical applications such as the development of personalized cancer vaccines, the discovery of biomarkers for response to checkpoint blockade and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 mono-allelic cell lines and created Systematic HLA Epitope Ranking Pan Algorithm (SHERPA™), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale mono-allelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA alleles to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC binding pocket diversity in the training data and extend allelic coverage in underprofiled populations. To improve generalizability, SHERPA systematically integrates 128 mono-allelic and 384 multi-allelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multi-allelic deconvolution and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44 fold improvement of positive predictive value compared to existing tools when evaluated on independent mono-allelic datasets and a 1.17 fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.

Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation

Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anticancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass-spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past two decades. However, improvement in the sensitivity and specificity of prediction algorithms is needed for clinical applications such as the development of personalized cancer vaccines, the discovery of biomarkers for response to checkpoint blockade, and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 monoallelic cell lines and created Systematic HLA Epitope Ranking Pan Algorithm (SHERPA), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale monoallelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA alleles to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC-binding pocket diversity in the training data and extend allelic coverage in under profiled populations. To improve generalizability, SHERPA systematically integrates 128 monoallelic and 384 multiallelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution, and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44-fold improvement of positive predictive value compared with existing tools when evaluated on independent monoallelic datasets and a 1.15-fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.

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Generated 25 stably transfected monoallelic cell lines and applied immunopeptidomics.

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Harmonized 512 public immunopeptidomic samples through systematic reprocessing.

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Developed pan-allele MHC-binding algorithm (SHERPA) utilizing 167 human HLA alleles.

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SHERPA demonstrates up to 1.44-fold increased precision over competing algorithms.

Menopause and cognitive complaints: are ovarian hormones linked with subjective cognitive decline?

Subjective cognitive decline (SCD) and the loss of ovarian hormones after menopause have been independently linked to later-life Alzheimer's disease (AD). The objective of this review was to determine whether menopause and the loss of ovarian hormones contribute to cognitive complaints and SCD in women. This would suggest that SCD at the menopausal transition might be an important marker of eventual cognitive decline and AD. We conducted a literature search using PubMed, PsycINFO and Web of Science in July 2020. All English-language studies assessing SCD and cognitive complaints with respect to menopause and ovarian hormones were included. A total of 19 studies were included. Studies found that cognitive complaints increased across the menopause transition and were associated with reductions in attention, verbal and working memory, and medial temporal lobe volume. Women taking estrogen-decreasing treatments also had increased cognitive complaints and reduced working memory and executive function. The current literature provides impetus for further research on whether menopause and the loss of ovarian hormones are associated with cognitive complaints and SCD. Clinicians may take particular note of cognitive complaints after menopause or ovarian hormone loss, as they might presage future cognitive decline.

Hearing loss is associated with gray matter differences in older adults at risk for and with Alzheimer's disease

Using data from the COMPASS-ND study we investigated associations between hearing loss and hippocampal volume as well as cortical thickness in older adults with subjective cognitive decline (SCD), mild cognitive impairment (MCI), and Alzheimer's dementia (AD). SCD participants with greater pure-tone hearing loss exhibited lower hippocampal volume, but more cortical thickness in the left superior temporal gyrus and right pars opercularis. Greater speech-in-noise reception thresholds were associated with lower cortical thickness bilaterally across much of the cortex in AD. The AD group also showed a trend towards worse speech-in-noise thresholds compared to the SCD group.

qPCRTag Analysis--A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic chromosome, synIII(1), and one synthetic chromosome arm, synIXR(2), have been constructed and their in vivo function validated in the absence of the corresponding wild type chromosomes. An important design feature of Sc2.0 chromosomes is the introduction of PCRTags, which are short, re-coded sequences within open reading frames (ORFs) that enable differentiation of synthetic chromosomes from their wild type counterparts. PCRTag primers anneal selectively to either synthetic or wild type chromosomes and the presence/absence of each type of DNA can be tested using a simple PCR assay. The standard readout of the PCRTag assay is to assess presence/absence of amplicons by agarose gel electrophoresis. However, with an average PCRTag amplicon density of one per 1.5 kb and a genome size of ~12 Mb, the completed Sc2.0 genome will encode roughly 8,000 PCRTags. To improve throughput, we have developed a real time PCR-based detection assay for PCRTag genotyping that we call qPCRTag analysis. The workflow specifies 500 nl reactions in a 1,536 multiwell plate, allowing us to test up to 768 PCRTags with both synthetic and wild type primer pairs in a single experiment.

Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae

We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae. Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform homologous recombination and efficiently join sequences with terminal homology. In the VEGAS workflow, terminal homology between adjacent pathway genes and the assembly vector is encoded by 'VEGAS adapter' (VA) sequences, which are orthogonal in sequence with respect to the yeast genome. Prior to pathway assembly by VEGAS in S. cerevisiae, each gene is assigned an appropriate pair of VAs and assembled using a previously described technique called yeast Golden Gate (yGG). Here we describe the application of yGG specifically to building transcription units for VEGAS assembly as well as the VEGAS methodology. We demonstrate the assembly of four-, five- and six-gene pathways by VEGAS to generate S. cerevisiae cells synthesizing β-carotene and violacein. Moreover, we demonstrate the capacity of yGG coupled to VEGAS for combinatorial assembly.

Hyperthermia induces injury to the intestinal mucosa in the mouse: evidence for an oxidative stress mechanism

Loss of the intestinal barrier is critical to the clinical course of heat illness, but the underlying mechanisms are still poorly understood. We tested the hypothesis that conditions characteristic of mild heatstroke in mice are associated with injury to the epithelial lining of the intestinal tract and comprise a critical component of barrier dysfunction. Anesthetized mice were gavaged with 4 kDa FITC-dextran (FD-4) and exposed to increasing core temperatures, briefly reaching 42.4°C, followed by 30 min recovery. Arterial samples were collected to measure FD-4 concentration in plasma (in vivo gastrointestinal permeability). The small intestines were then removed to measure histological evidence of injury. Hyperthermia resulted in a ≈2.5-fold elevation in plasma FD-4 and was always associated with significant histological evidence of injury to the epithelial lining compared with matched controls, particularly in the duodenum. When isolated intestinal segments from control animals were exposed to ≥41.5°C, marked increases in permeability were observed within 60 min. These changes were associated with release of lactate dehydrogenase, evidence of protein oxidation via carbonyl formation and histological damage. Coincubation with N-acetylcysteine protected in vitro permeability during hyperthermia and reduced histological damage and protein oxidation. Chelation of intracellular Ca(2+) to block tight junction opening during 41.5°C exposure failed to reduce the permeability of in vitro segments. The results demonstrate that hyperthermia exposure in mouse intestine, at temperatures at or below those necessary to induce mild heatstroke, cause rapid and substantial injury to the intestinal lining that may be attributed, in part, to oxidative stress.

Female sexual dysfunction: evaluation and treatment

Sexual dysfunction includes desire, arousal, orgasmic and sex pain disorders (dyspareunia and vaginismus). Primary care physicians must assume a proactive role in the diagnosis and treatment of these disorders. Long-term medical diseases, minor ailments, medications and psychosocial difficulties, including prior physical or sexual abuse, are etiologic factors. Gynecologic maladies and cancers (including breast cancer) are also frequent sources of sexual dysfunction. Patient education and reassurance, with early diagnosis and intervention, are essential for effective treatment. Patient history and physical examination techniques, normal sexual responses and the factors that influence these responses, and the application of medical and gynecologic treatments to sexual issues are discussed. Basic treatment strategies, which may be successfully provided by primary care physicians for most sexual dysfunctions, are outlined. Referral can be reserved for patients who do not respond to therapy.

Age-related differences in semantic priming: evidence from event-related brain potentials

Hasher and Zacks (1988) suggested that aging may affect processes involved in the inhibition of irrelevant information during language processing. Our experiment tested this hypothesis using the N400 event-related brain potential in a priming paradigm and assessed whether older subjects could benefit from the constraints of a sentence context. Twenty older (63 to 88 years) and 20 young (19 to 29 years) subjects read sentences and word pairs. Each final word varied on the degree of relatedness to the preceding context, with some being highly related (BC), moderately related (R), or unrelated (U). Younger subjects showed the expected N400 effect gradient (U > R > BC) in both the sentence and word-pair contexts, while older adults showed no discrimination between the conditions (U = R = BC) for the sentence and limited discrimination (U > BC) for the word pairs. These results support the inhibition-deficit hypothesis, whereby older adults fail to inhibit related items in working memory, and suggest that older adults do not benefit from the constraints of a sentence context.

Oral phentolamine and female sexual arousal disorder: a pilot study

Female sexual arousal disorder (FSAD) is a highly prevalent problem, although little is known about pathophysiology or treatment of the disorder. Given the potential role of vascular mechanisms, a small pilot study was conducted on the effects of oral phentolamine in menopausal women with FSAD. Six postmenopausal women with a lack of lubrication and with sexual arousal difficulties of at least 6 months duration participated in the study. All subjects received a single dose of oral phentolamine (40 mg) and placebo in a single-blind, dose-escalation design. Dependent variables for the study included vaginal pulse amplitude (VPA), as measured by vaginal photoplethysmography, self-report measures of sexual response, and patient- and physician-based assessments of adverse events. Results indicated a mild, positive effect of phentolamine across all measures of arousal, with significant changes (p < .05) in self-reported lubrication and pleasurable sensations in the vagina. The drug was well tolerated, overall, with few reports of adverse side effects. Further studies are needed to assess the potential value of phentolamine and other vasoactive agents in the treatment of female sexual dysfunction.

The clinical evaluation of dyspareunia

Strictly defined, dyspareunia means 'pain with intercourse'. The psychiatric DSM-IV subdivides and expands this definition and introduces psychogenic factors into the differential diagnosis. This allows development of a biogenic-psychogenic model, whereby organic or psychological factors can be present separately or in combination, within the disorder. Sexual dysfunctions are estimated to be present in 19-63% of women, with dyspareunia the primary complaint in 8-48%. The clinical evaluation of dyspareunia should include a thorough history and meticulous gynecologic examination. Laboratory or imaging studies should be ordered as warranted by suggestive history or exam findings. Identified causes should be treated and counseling considered. Three clinical dilemmas remain. Firstly, lack of standardization of exam findings; secondly discrepancy between objective physical findings and subjective patient complaints; and thirdly paucity of therapeutic options for patients, especially those with an unclear diagnosis. An integrated psychogenic-biogenic model should be developed and implemented for effective diagnosis and treatment of dyspareunia.

Individual differences in auditory middle latency responses in elderly adults and patients with Alzheimer's disease

Previous research has suggested that the Pb component of the middle-latency auditory evoked response (MLAER) is differentially abnormal in patients with Alzheimer's disease relative to control subjects. In the present study, this putative abnormality was examined in vertex-recorded MLAERs elicited by monaural stimulation in 14 patients with Alzheimer's disease (six females) and 22 age-matched control subjects (10 females). A sex difference in Pb elicitation was revealed in control subjects; Pb area was twice as large in females than males (P < 0.05). Pb and Pa amplitudes and latencies did not differ between male and female control subjects. Comparisons of Pb between patients and controls were conducted within each sex. There was no main effect of group on Pb area, amplitude, or latency, Pa amplitude was significantly larger in patients than control subjects; there was no group difference in Pa latency. This study did not replicate previous reports of differences in Pb between patients with Alzheimer's disease and elderly control subjects. We demonstrated that Pb elicitation may be unreliable in elderly control subjects and found evidence of a possible sex difference. The effects of inter-subject variables (e.g. age, sex) must be understood more fully before MLAERs can be exploited as meaningful markers of brain dysfunction.

Cognitive deficits in peripheral vascular disease. A comparison of mild stroke patients and normal control subjects

BACKGROUND AND PURPOSE

Evidence indicates that peripheral vascular disease (PVD) and cerebrovascular disease (CVD) coexist and therefore reflect a generalized pattern of atherosclerotic disease in an individual. Given the known deleterious effects of CVD on cognitive function, it was hypothesized that patients with PVD may have impaired cerebral function due to concomitant but clinically unrecognized CVD. The purpose of this study was to determine whether neuropsychological tests would reveal this potential dysfunction.

METHODS

Neuropsychological test scores (n = 25) were compared across three groups: (1) 29 PVD patients (13 amputees, 16 nonamputees), (2) 29 age- and education-matched patients with atherothrombotic brain infarcts (ie, CVD), and (3) 30 age- and education-matched control subjects.

RESULTS

PVD patients performed significantly worse (P < .002) than control subjects on eight neuropsychological measures of executive function, attention, and visuopatial function. The pattern and, in certain instances, the magnitude of impairment was highly similar between PVD and CVD subjects. Regression analysis revealed that PVD severity and ischemic heart disease were significant negative predictors of test performance. Depression and atherosclerotic risk factors did not explain neuropsychological deficits after the effects of PVD and ischemic heart disease were considered.

CONCLUSIONS

PVD patients exhibit neuropsychological deficits that suggest the presence of mild vascular-related brain dysfunction. Patients with multiple manifestations of generalized atherosclerosis (ie, severe PVD, ischemic heart disease) appear to be particularly at risk. Clinicians should be alert to these potential deficits and to the possibility of further vascular-related cognitive decline.

Grouped data do not tell the whole story: individual analysis of cognitive change after temporal lobectomy

Studies of group measures of central tendency describe the cognitive sequelae of anterior temporal lobectomy; however, information regarding clinically significant change is scarce. This study examined the frequency of clinically significant variability (i.e., a change score > or = 1 standard deviation from preoperative to postoperative performance) in 50 temporal lobectomy patients (19 left-sided; 31 right-sided). A range of cognitive domains was examined. Most (68%) indices showed no change. Of those that changed, an approximately equivalent number were losses and gains. Such results do not support restricting surgical treatment of epilepsy to avoid major cognitive decline. In right-handers, the observance of material-specific memory decline was variable. Only 36% of right-handers with left-temporal lobectomy showed only postsurgical loss in verbal memory, while 50% showed both losses and gains across several verbal memory measures. Almost 60% of right-temporal lobectomy patients exhibited some verbal memory loss, but only one-third showed nonverbal memory loss. We conclude that group studies identifying material-specific memory loss overestimate the consistency and pervasiveness of the negative effects of temporal lobectomy.

The effects of phonological and semantic features of sentence-ending words on visual event-related brain potentials

Event-related brain potentials (ERPs) were recorded to terminal words of visually presented sentences that were identical to those used in an auditory modality study examining the effects of phonological and semantic characteristics of words on ERPs (Connolly and Phillips, 1994). Phonological and/or semantic characteristics of terminal words were manipulated in 4 conditions in which: (1) the terminal word was the highest cloze probability ending for the sentence and was thus phonologically and semantically appropriate to the sentence context (e.g., Ray fell down and skinned his knee(s).; (2) the terminal word had the initial phonemic sound of the highest cloze probability sentence-ending word but was semantically anomalous to the context of the sentence (e.g., They sat together without saying a single worm. [word]); (3) the initial phoneme of the terminal word was phonologically unexpected but the word was semantically correct (e.g., The dough was put in the hot pan. [oven]); or (4) the initial phoneme of the terminal word was phonologically unexpected and the word was semantically inappropriate to the sentence context (e.g., Bill jumped into the lake and made a big farm. [splash]). A left fronto-temporally distributed negative peak was observed in the 250-300 msec range to varying degrees in all conditions but was largest in the condition in which terminal words were both phonologically unexpected and semantically inappropriate. A second, parietally distributed, symmetrical negativity (the N400) was found which peaked around 365 msec and was largest in the two conditions involving semantically anomalous terminal words. Results are discussed in terms of modality factors in ERP manifestations of receptive language functions and the implications of ERP modality differences for theories of word recognition.

Neuropsychological function in peripheral vascular disease amputee patients

Approximately 75% of major lower-extremity amputations are the result of peripheral vascular disease (PVD). Factors that predispose a patient to PVD (smoking, hyperlipidemia, diabetes mellitus) are also risk factors for the development of cerebrovascular disease, which could adversely affect rehabilitation. The purpose of this study was to test the hypothesis that cognitive deficits are present in amputee patients with PVD. Fourteen patients with lower-extremity amputations secondary to PVD (4 women, 10 men; mean age = 67.4 years) were recruited from a tertiary-care center for physical rehabilitation. Fourteen community-dwelling healthy volunteers (9 women, 5 men; mean age = 69.9 years) served as age-matched and education-matched controls. To assess a broad range of cognitive function, we administered standard neuropsychological tests of memory and learning, language, praxis, visuospatial skills, and abstract reasoning. PVD patients performed significantly more poorly on certain measures of psychomotor speed (Wechsler Adult Intelligence Scale-Revised Digit Symbol subtest) and problem solving/abstract reasoning (Modified Card Sorting Test) relative to controls (using the Bonferroni correction for multiple comparisons, p < .002). There were trends toward poorer patient performance on certain measures of oral fluency, concentration, reasoning, and visuoperceptual organization and constructional skills (p < .01). We propose that these cognitive deficits may be the result of unrecognized concomitant cerebrovascular disease in PVD patients and are part of a generalized pattern of vascular disease. Future research should control affective factors such as stress or depression surrounding amputation and attempt to identify the etiologic or demographic factors that are associated with neuropsychological deficits in patients with PVD.