Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer

Introduction

We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer.

Method

We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot).

Results

We uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5'-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3' through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response.

Conclusion

Our data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion.

Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity

Identifying neoepitopes that elicit an adaptive immune response is a major bottleneck to developing personalized cancer vaccines. Experimental validation of candidate neoepitopes is extremely resource intensive and the vast majority of candidates are non-immunogenic, creating a needle-in-a-haystack problem. Here we address this challenge, presenting computational methods for predicting class I major histocompatibility complex (MHC-I) epitopes and identifying immunogenic neoepitopes with improved precision. The BigMHC method comprises an ensemble of seven pan-allelic deep neural networks trained on peptide-MHC eluted ligand data from mass spectrometry assays and transfer learned on data from assays of antigen-specific immune response. Compared with four state-of-the-art classifiers, BigMHC significantly improves the prediction of epitope presentation on a test set of 45,409 MHC ligands among 900,592 random negatives (area under the receiver operating characteristic = 0.9733; area under the precision-recall curve = 0.8779). After transfer learning on immunogenicity data, BigMHC yields significantly higher precision than seven state-of-the-art models in identifying immunogenic neoepitopes, making BigMHC effective in clinical settings.

Abstract 1393: Persistent mutation burden drives sustained anti-tumor immune responses in human cancers

INTRODUCTION: Tumor mutation burden (TMB) is a commonly used biomarker for cancer immunotherapy however TMB only partially captures tumor foreignness. We hypothesized that mutations in single-copy regions of the genome or mutations present in multiple copies (hereafter referred to as persistent mutations) are retained during cancer evolution and immunoediting, may render the tumor continuously visible to the immune system and promote sustained tumor control during immune checkpoint blockade (ICB).

METHODS: We performed pan-cancer analyses of whole exome sequencing data across 31 tumor types in TCGA to quantify the landscape of persistent mutations (n=9,242). We then evaluated the association between persistent tumor mutation burden (pTMB) and ICB response compared to TMB in eight ICB-treated cohorts of patients with NSCLC, melanoma, mesothelioma, and head and neck cancer (n=524). To investigate the clonal evolution of persistent mutations we serially analyzed whole exome sequence data from NSCLCs prior to and at emergence of acquired resistance to ICB. Finally, we evaluated the composition of the tumor microenvironment (TME) in baseline and on-ICB melanomas by RNA sequencing differential enrichment analyses and deconvolution.

RESULTS: Integration of sequence alterations in only-copy and multi-copy states for 9,242 tumors across 31 tumor types revealed a cancer lineage-dependent distribution of persistent mutations that was largely independent of the overall TMB. In evaluating differential classification based on pTMB- vs TMB-high, we found re-classification rates as high as 53% in individual tumor types, with a median reclassification rate of 33% across all tumor types (range 15% - 53%). We then evaluated the clonal composition of persistent mutations and found a wide range of correlations between pTMB and fraction of clonal mutations (Spearman ρ range: -0.11 - 0.59). In ICB-treated cohorts, pTMB better distinguished responding tumors compared to TMB, and a number of mutation and copy-number related features including tumor aneuploidy (melanoma: Mann-Whitney p=2.3e-06, NSLC: p&lt;2.0e-03, mesothelioma p=0.03, HNSCC p=0.05). Using in silico simulations, we found a similar advantage for pTMB when estimated from gene-panel targeted next generation sequencing. To support the biological plausibility of pTMB in the context of tumor evolution, we evaluated the rate loss of persistent mutations in longitudinal analyses of pre- and post-ICB NSCLC and found that a rate of loss significantly lower for persistent compared to loss-prone mutations (odds ratio 61.43, p&lt;2.2e-16). Consistent with our hypothesis, pTMB-high tumors had a more inflamed TME (p&lt;1e-11).

CONCLUSIONS: Persistent mutations represent a biologically distinct subset within the overall TMB that is unlikely to be lost under selective pressure of ICB and may function as an intrinsic driver of sustained immunologic tumor control.

Citation Format: Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M. Shao, Zineb Belcaid, Kristen A. Marrone, Joseph Murray, Kellie N. Smith, Benjamin Levy, Josephine Feliciano, Christine L. Hann, Vincent Lam, Drew M. Pardoll, Rachel Karchin, Tanguy Y. Seiwert, Julie R. Brahmer, Patrick M. Forde, Victor E. Velculescu, Valsamo K. Anagnostou. Persistent mutation burden drives sustained anti-tumor immune responses in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1393.

Persistent mutation burden drives sustained anti-tumor immune responses

Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed to consistently demonstrate clinical utility in predicting responses in the context of immunotherapy. We evaluated mutations in regions of the genome that are unlikely to undergo loss in a pan-cancer analysis across 31 tumor types (n = 9,242) and eight immunotherapy-treated cohorts of patients with non-small-cell lung cancer, melanoma, mesothelioma, and head and neck cancer (n = 524). We discovered that mutations in single-copy regions and those present in multiple copies per cell constitute a persistent tumor mutation burden (pTMB) which is linked with therapeutic response to immune checkpoint blockade. Persistent mutations were retained in the context of tumor evolution under selective pressure of immunotherapy and tumors with a high pTMB content were characterized by a more inflamed tumor microenvironment. pTMB imposes an evolutionary bottleneck that cancer cells cannot overcome and may thus drive sustained immunologic tumor control in the context of immunotherapy.

Sex-specific differences in immunogenomic features of response to immune checkpoint blockade

Introduction

The magnitude of response to immune checkpoint inhibitor (ICI) therapy may be sex-dependent, as females have lower response rates and decreased survival after ICI monotherapy. The mechanisms underlying this sex dimorphism in ICI response are unknown, and may be related to sex-driven differences in the immunogenomic landscape of tumors that shape anti-tumor immune responses in the context of therapy.

Methods

To investigate the association of immunogenic mutations with HLA haplotypes, we leveraged whole exome sequence data and HLA genotypes from 482 non-small cell lung cancer (NSCLC) tumors from The Cancer Genome Atlas (TCGA). To explore sex-specific genomic features linked with ICI response, we analyzed whole exome sequence data from patients with NSCLC treated with ICI. Tumor mutational burden (TMB), HLA class I and II restricted immunogenic missense mutation (IMM) load, and mutational smoking signature were defined for each tumor. IMM load was combined with HLA class I and II haplotypes and correlated with therapeutic response and survival following ICI treatment. We examined rates of durable clinical benefit (DCB) for at least six months from ICI treatment initiation. Findings were validated utilizing whole exome sequence data from an independent cohort of ICI treated NSCLC.

Results

Analysis of whole exome sequence data from NSCLC tumors of females and males revealed that germline HLA class II diversity (≥9 unique HLA alleles) was associated with higher tumor class II IMM load in females (p=0.01) and not in males (p=0.64). Similarly, in tumors of female patients, somatic HLA class II loss of heterozygosity was associated with increased IMM load (p=0.01) while this association was not observed in tumors in males (p=0.20). In females, TMB (p=0.005), class I IMM load (p=0.005), class II IMM load (p=0.004), and mutational smoking signature (p<0.001) were significantly higher in tumors responding to ICI as compared to non-responding tumors. In contrast, among males, there was no significant association between DCB and any of these features. When IMM was considered in the context of HLA zygosity, high MHC-II restricted IMM load and high HLA class II diversity was significantly associated with overall survival in males (p=0.017).

Conclusions

Inherent sex-driven differences in immune surveillance affect the immunogenomic determinants of response to ICI and likely mediate the dimorphic outcomes with ICI therapy. Deeper understanding of the selective pressures and mechanisms of immune escape in tumors in males and females can inform patient selection strategies and can be utilized to further hone immunotherapy approaches in cancer.

HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade

BACKGROUND

Whereas human leukocyte antigen (HLA) class I mutation-associated neoantigen burden has been linked with response to immune checkpoint blockade (ICB), the role of HLA class II-restricted neoantigens in clinical responses to ICB is less studied. We used computational approaches to assess HLA class II immunogenic mutation (IMM) burden in patients with melanoma and lung cancer treated with ICB.

PATIENTS AND METHODS

We analyzed whole-exome sequence data from four cohorts of ICB-treated patients with melanoma (n = 110) and non-small-cell lung cancer (NSCLC) (n = 123). MHCnuggets, a neural network-based model, was applied to estimate HLA class II IMM burdens and cellular fractions of IMMs were calculated to assess mutation clonality. We evaluated the combined impact of HLA class II germline genetic variation and class II IMM burden on clinical outcomes. Correlations between HLA class II IMM burden and density of tumor-infiltrating lymphocytes were computed from expression data.

RESULTS

Responding tumors harbored a significantly higher HLA class II IMM burden for both melanoma and NSCLC (P ≤ 9.6e-3). HLA class II IMM burden was correlated with longer survival, particularly in the NSCLC cohort and in the context of low intratumoral IMM heterogeneity (P < 0.001). HLA class I and II IMM landscapes were largely distinct suggesting a complementary role for class II IMMs in tumor rejection. A higher HLA class II IMM burden was associated with CD4+ T-cell infiltration and programmed death-ligand 1 expression. Transcriptomic analyses revealed an inflamed tumor microenvironment for tumors harboring a high HLA class II IMM burden.

CONCLUSIONS

HLA class II IMM burden identified patients with NSCLC and melanoma that attained longer survival after ICB treatment. Our findings suggest that HLA class II IMMs may impact responses to ICB in a manner that is distinct and complementary to HLA class I-mediated responses.

Abstract 1617: Sex-specific genomic determinants of response to immunotherapy

Introduction: The magnitude of benefit from immune checkpoint inhibitors (ICI) may be sex-dependent, however the mechanisms underlying this sex dimorphism in ICI response are unknown.

Methods: To explore sex-specific genomic features linked with ICI response, we analyzed whole-exome sequence data of 89 patients with non-small cell lung cancer (NSCLC) treated with ICI. Sequence alteration, mutation signatures and clonality analyses were combined with HLA class I and II genotyping, and computationally derived mutation-associated neoantigens were evaluated based on the peptide-HLA binding affinity (&lt;500nM) and the relative binding affinity between mutated and wild-type peptides [quotient differential aggretopic index (qDAI) &gt;2]. Missense sequence alterations were characterized as putatively immunogenic mutations (IMM), and HLA class I and II matched IMM loads were calculated. Durable clinical benefit ≥6 months was used to define response. Our findings were validated in an independent cohort of ICI treated NSCLC (n=34).

Results: There were no differences in the genomic features assessed or in clinical outcomes between male (n=46) and female (n=43) patients. Female responders had higher tumor mutational burden (TMB; p=0.004), in contrast to male patients (p=0.15). Similarly, a mutation spectra-derived smoking signature was associated with response in females (p=0.001) but not in males (p=0.2). Responding female patients had a more clonal TMB compared to non-responders (p=0.008). Importantly, female responders harbored a significantly higher class I and II IMM load (p=0.008 and p=0.004 respectively), which was not appreciated in males. These findings were supported by analyses of a second independent cohort, where HLA class I and II IMM load differentiated responders from non-responders only in the female patient group (p=0.008 and p=0.004 for class I and II IMM, respectively). In the primary cohort, germline HLA class I zygosity was not associated with outcome for either sex, however a trend towards HLA DQ-B1 homozygosity and worse outcome was evident only in females. Importantly, when HLA class II diversity was combined with class II IMM load, a survival benefit was noted for tumors harboring a high IMM load and maximal HLA II germline diversity in males (log rank p=0.015) but not in females. Similarly, HLA class I diversity was important in males when combined with class I IMM load, such that low IMM load combined with reduced antigen presentation capacity was predictive of non-durable clinical benefit (p=0.003 vs p=0.68 for males and females respectively) and was linked with shorter overall survival (log rank p= 0.062 vs p=0.58 for males and females respectively).

Conclusions: Our findings support a sex dimorphism in the genomic determinants of response to immune checkpoint blockade, which may point to differences in immune surveillance between males and females in the context of therapy and may be used to tailor therapeutic delivery.

Citation Format: Susan C. Scott, Xiaoshan M. Shao, Noushin Niknafs, Archana Balan, Mara Lanis, James White, Patrick Forde, Kristen Marrone, Vincent Lam, Josephine Feliciano, Benjamin Levy, Julie Brahmer, David Ettinger, Victor Velculescu, Rachel Karchin, Christine Hann, Jarushka Naidoo, Valsalmo Anagnostou. Sex-specific genomic determinants of response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1617.

Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma

In this study, we incorporate analyses of genome-wide sequence and structural alterations with pre- and on-therapy transcriptomic and T cell repertoire features in immunotherapy-naive melanoma patients treated with immune checkpoint blockade. Although tumor mutation burden is associated with improved treatment response, the mutation frequency in expressed genes is superior in predicting outcome. Increased T cell density in baseline tumors and dynamic changes in regression or expansion of the T cell repertoire during therapy distinguish responders from non-responders. Transcriptome analyses reveal an increased abundance of B cell subsets in tumors from responders and patterns of molecular response related to expressed mutation elimination or retention that reflect clinical outcome. High-dimensional genomic, transcriptomic, and immune repertoire data were integrated into a multi-modal predictor of response. These findings identify genomic and transcriptomic characteristics of tumors and immune cells that predict response to immune checkpoint blockade and highlight the importance of pre-existing T and B cell immunity in therapeutic outcomes.

Unmet need for integrated molecular models that interpret immunotherapy response

Genomic, transcriptomic, and T and B cell sequence data integration by machine learning

T cell dynamism is a hallmark of response to immune checkpoint blockade

The combined contributions of B, T, and tumor cell features predict clinical outcome

Abstract A33: High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets

Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins is an emerging biomarker for predicting patient response to cancer immunotherapy. Current neoantigen predictors focus on in silico estimation of MHC binding affinity and are limited by low positive predictive value for actual peptide presentation, inadequate support for rare MHC alleles, and poor scalability to high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep neural network method to predict peptide-MHC binding. MHCnuggets is the only method to handle binding prediction for common or rare alleles of MHC Class I or II, with a single neural network architecture. Using a long short-term memory network (LSTM), MHCnuggets accepts peptides of variable length and is capable of faster performance than other methods. When compared to methods that integrate binding affinity and HLAp data from mass spectrometry, MHCnuggets yields a fourfold increase in positive predictive value on independent MHC-bound peptide (HLAp) data. We applied MHCnuggets to 26 cancer types in TCGA, processing 52.6 million allele-peptide comparisons in under 2.3 hours, yielding 103,587 candidate immunogenic missense mutations (IMMs). IMM hotspots occurred in 36 genes, including 22 driver genes. Predicted IMM load was significantly associated with increased immune cell infiltration (p&lt;2e-16), including CD8+ T cells. Notably, only 0.15% of predicted immunogenic missense mutations were observed in &gt;2 patients, with 65% of these derived from driver mutations. Our results provide a new method for neoantigen prediction with high performance characteristics and demonstrate its utility in large data sets across human cancers.

Citation Format: Xiaoshan M. Shao, Rohit Bhattacharya, Justin Huang, Ashok Sivakumar, Collin Tokheim, Lily Zheng, Dylan Hirsch, Ben Kaminow, Ashton Omdahl, Maria Bonsack, Angelika B. Riemer, Victor E. Velculescu, Valsamo Anagnostou, Kymberleigh Pagel, Rachel Karchin. High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A33.

High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets

Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response to cancer immunotherapy. Current neoantigen predictors focus on in silico estimation of MHC binding affinity and are limited by low predictive value for actual peptide presentation, inadequate support for rare MHC alleles, and poor scalability to high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep neural network method that predicts peptide-MHC binding. MHCnuggets can predict binding for common or rare alleles of MHC class I or II with a single neural network architecture. Using a long short-term memory network (LSTM), MHCnuggets accepts peptides of variable length and is faster than other methods. When compared with methods that integrate binding affinity and MHC-bound peptide (HLAp) data from mass spectrometry, MHCnuggets yields a 4-fold increase in positive predictive value on independent HLAp data. We applied MHCnuggets to 26 cancer types in The Cancer Genome Atlas, processing 26.3 million allele-peptide comparisons in under 2.3 hours, yielding 101,326 unique predicted immunogenic missense mutations (IMM). Predicted IMM hotspots occurred in 38 genes, including 24 driver genes. Predicted IMM load was significantly associated with increased immune cell infiltration (P < 2 × 10^-16), including CD8⁺ T cells. Only 0.16% of predicted IMMs were observed in more than 2 patients, with 61.7% of these derived from driver mutations. Thus, we describe a method for neoantigen prediction and its performance characteristics and demonstrate its utility in data sets representing multiple human cancers.

Cholinergic neurotransmission in the preBötzinger Complex modulates excitability of inspiratory neurons and regulates respiratory rhythm

We investigated whether there is endogenous acetylcholine (ACh) release in the preBötzinger Complex (preBötC), a medullary region hypothesized to contain neurons generating respiratory rhythm, and how endogenous ACh modulates preBötCneuronal function and regulates respiratory pattern. Using a medullary slice preparation from neonatal rat, we recorded spontaneous respiratory-related rhythm from the hypoglossal nerve roots (XIIn) and patch-clamped preBötC inspiratory neurons. Unilateral microinjection of physostigmine, an acetylcholinesterase inhibitor, into the preBötC increased the frequency of respiratory-related rhythmic activity from XIIn to 116+/-13% (mean+/-S.D.) of control. Ipsilateral physostigmine injection into the hypoglossal nucleus (XII nucleus) induced tonic activity, increased the amplitude and duration of the integrated inspiratory bursts of XIIn to 122+/-17% and 117+/-22% of control respectively; but did not alter frequency. In preBötC inspiratory neurons, bath application of physostigmine (10 microM) induced an inward current of 6.3+/-10.6 pA, increased the membrane noise, decreased the amplitude of phasic inspiratory drive current to 79+/-16% of control, increased the frequency of spontaneous excitatory postsynaptic currents to 163+/-103% and decreased the whole cell input resistance to 73+/-22% of control without affecting the threshold for generation of action potentials. Bath application of physostigmine concurrently induced tonic activity, increased the frequency, amplitude and duration of inspiratory bursts of XIIn motor output. Bath application of 4-diphenylacetoxy-N-methylpiperidine methiodide (4-DAMP, 2 microM), a M3 muscarinic acetylcholine receptor (mAChR) selective antagonist, increased the input resistance of preBötC inspiratory neurons to 116+/-9% of control and blocked all of the effects of physostigmine except for the increase in respiratory frequency. Dihydro-beta-erythroidine (DH-beta-E; 0.2 microM), an alpha4beta2 nicotinic receptor (nAChR) selective antagonist, blocked all the effects of physostigmine except for the increase in inspiratory burst amplitude. In the presence of both 4-DAMP and DH-beta-E, physostigmine induced opposite effects, i.e. a decrease in frequency and amplitude of XIIn rhythmic activity. These results suggest that there is cholinergic neurotransmission in the preBötC which regulates respiratory frequency, and in XII nucleus which regulates tonic activity, and the amplitude and duration of inspiratory bursts of XIIn in neonatal rats. Physiologically relevant levels of ACh release, via mAChRs antagonized by 4-DAMP and nAChRs antagonized by DH-beta-E, modulate the excitability of inspiratory neurons and excitatory neurotransmission in the preBötC, consequently regulating respiratory rhythm.

One-third of term babies after perinatal hypoxia-ischaemia have transient hearing impairment: dynamic change in hearing threshold during the neonatal period

AIM

To examine the process of change in hearing threshold during the neonatal period after perinatal hypoxia-ischaemia.

METHODS

The threshold of brainstem auditory evoked responses (BAER) was measured serially during the first month after birth in 92 term babies who suffered hypoxia-ischaemia.

RESULTS

The mean BAER threshold in these babies was significantly increased on day 1 (ANOVA p < 0.001). The elevated threshold decreased progressively on days 3 and 5, but was still significantly higher than that in normal controls (p < 0.01). The elevation continuously decreased more slowly on days 10 and 15, and to a near normal level on day 30. Threshold elevation was seen in 31.7% of the babies on day 1, and 34.5% during the first three days. The rate of elevation decreased progressively thereafter. On day 30, 10.6% of the subjects still had increased thresholds. Moderate to severe elevation occurred mainly during the first week and severe elevation occurred predominately on day 1. Threshold elevation starting after days 3-5 is likely to be due to middle-ear disorders. As a whole, during the first month, 44.6% (41/92) of the babies studied had threshold elevation. BAER threshold was correlated weakly with the stage of hypoxic-ischaemic encephalopathy on days 1 and 3. The threshold was significantly higher in babies with severe encephalopathy than in those with mild or moderate encephalopathy during the first 3 d of life.

CONCLUSION

Hearing threshold is elevated in about one-third of term babies after hypoxia-ischaemia. The elevated threshold decreases progressively after birth, and returns to normal by one month in most babies. The threshold correlates weakly with the severity of encephalopathy.

RT-PCR reveals muscarinic acetylcholine receptor mRNA in the pre-Bötzinger complex

Muscarinic receptors mediate the postsynaptic excitatory effects of acetylcholine (ACh) on inspiratory neurons in the pre-Bötzinger complex (pre-BötC), the hypothesized site for respiratory rhythm generation. Because pharmacological tools for identifying the subtypes of the muscarinic receptors that underlie these effects are limited, we probed for mRNA for these receptors in the pre-BötC. We used RT-PCR to determine the expression of muscarinic receptor subtypes in tissue punches of the pre-BötC taken from rat medullary slices. Cholinergic receptor subtype M(2) and M(3) mRNAs were observed in the first round of PCR amplification. All five subtypes, M(1)-M(5), were observed in the second round of amplification. Our results suggest that the majority of muscarinic receptor subtypes in the pre-BötC are M(2) and M(3), with minor expression of M(1), M(4), and M(5).

Mechanisms underlying regulation of respiratory pattern by nicotine in preBötzinger complex

Cholinergic neurotransmission plays a role in regulation of respiratory pattern. Nicotine from cigarette smoke affects respiration and is a risk factor for sudden infant death syndrome (SIDS) and sleep-disordered breathing. The cellular and synaptic mechanisms underlying this regulation are not understood. Using a medullary slice preparation from neonatal rat that contains the preBötzinger Complex (preBötC), the hypothesized site for respiratory rhythm generation, and generates respiratory-related rhythm in vitro, we examined the effects of nicotine on excitatory neurotransmission affecting inspiratory neurons in preBötC and on the respiratory-related motor activity from hypoglossal nerve (XIIn). Microinjection of nicotine into preBötC increased respiratory frequency and decreased the amplitude of inspiratory bursts, whereas when injected into XII nucleus induced a tonic activity and an increase in amplitude but not in frequency of inspiratory bursts from XIIn. Bath application of nicotine (0.2--0.5 microM, approximately the arterial blood nicotine concentration immediately after smoking a cigarette) increased respiratory frequency up to 280% of control in a concentration-dependent manner. Nicotine decreased the amplitude to 82% and increased the duration to 124% of XIIn inspiratory bursts. In voltage-clamped preBötC inspiratory neurons (including neurons with pacemaker properties), nicotine induced a tonic inward current of -19.4 +/- 13.4 pA associated with an increase in baseline noise. Spontaneous excitatory postsynaptic currents (sEPSCs) present during the expiratory period increased in frequency to 176% and in amplitude to 117% of control values; the phasic inspiratory drive inward currents decreased in amplitude to 66% and in duration to 89% of control values. The effects of nicotine were blocked by mecamylamine (Meca). The inspiratory drive current and sEPSCs were completely eliminated by 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) in the presence or absence of nicotine. In the presence of tetrodotoxin (TTX), low concentrations of nicotine did not induce any tonic current or any increase in baseline noise, nor affect the input resistance in inspiratory neurons. In this study, we demonstrated that nicotine increased respiratory frequency and regulated respiratory pattern by modulating the excitatory neurotransmission in preBötC. Activation of nicotinic acetylcholine receptors (nAChRs) enhanced the tonic excitatory synaptic input to inspiratory neurons including pacemaker neurons and at the same time, inhibited the phasic excitatory coupling between these neurons. These mechanisms may account for the cholinergic regulation of respiratory frequency and pattern.

Electrical coupling and excitatory synaptic transmission between rhythmogenic respiratory neurons in the preBötzinger complex

Breathing pattern is postulated to be generated by brainstem neurons. However, determination of the underlying cellular mechanisms, and in particular the synaptic interactions between respiratory neurons, has been difficult. Here we used dual recordings from two distinct populations of brainstem respiratory neurons, hypoglossal (XII) motoneurons, and rhythmogenic (type-1) neurons in the preBötzinger complex (preBötC), the hypothesized site for respiratory rhythm generation, to determine whether electrical and chemical transmission is present. Using an in vitro brainstem slice preparation from newborn mice, we found that intracellularly recorded pairs of XII motoneurons and pairs of preBötC inspiratory type-1 neurons showed bidirectional electrical coupling. Coupling strength was low (<0.10), and the current that passed between two neurons was heavily filtered (corner frequency, <10 Hz). Dual recordings also demonstrated unidirectional excitatory chemical transmission (EPSPs of approximately 3 mV) between type-1 neurons. These data indicate that respiratory motor output from the brainstem involves gap junction-mediated current transfer between motoneurons. Furthermore, bidirectional electrical coupling and unidirectional excitatory chemical transmission are present between type-1 neurons in the preBötC and may be important for generation or modulation of breathing rhythm.

Maximum length sequence brainstem auditory evoked responses in term neonates who have perinatal hypoxia-ischemia

Maximum length sequence brainstem auditory evoked response (BAER) was studied within the first week after birth in 28 term neonates who had perinatal hypoxia-ischemia, or asphyxia. In the BAER recorded using conventional averaging techniques (click rate 21/s), the only abnormality was a slight increase in III-V interval, in addition to an increase in wave latencies when including those who had an elevated threshold (t test, all p<0.05). In the maximum length sequence BAER, however, both the III-V and I-V intervals in the asphyxiated infants were significantly increased at all the 91/s, 227/s, 455/s, and particularly 910/s click rates (p<0.05-0.001). The I-III interval was also increased significantly at 455/s and 910/s click rates (both p< 0.05). Wave V amplitude was significantly reduced at all the click rates used (ANOVA, p<0.05-0.001), particularly at 910/s, which sometimes was the only abnormality indicative of brain damage. Both the amplitude ratios V/I and V/III were significantly decreased at 455/s and 910/s click rates (p<0.01 or 0.001). A general trend was that BAER abnormalities after hypoxia-ischemia became more prominent as click rate was increased. Significant abnormalities occurred mainly at very high click rates (455/s and 910/s), which can be achieved using the maximum length sequence technique but not by using conventional averaging techniques. Thus, this technique, which can be used at the cribside, appears to be a better method for the early detection of brain damage after hypoxia-ischemia than using conventional averaging techniques, enhancing the diagnostic value of the BAER.

Acetylcholine modulates respiratory pattern: effects mediated by M3-like receptors in preBötzinger complex inspiratory neurons

Perturbations of cholinergic neurotransmission in the brain stem affect respiratory motor pattern both in vivo and in vitro; the underlying cellular mechanisms are unclear. Using a medullary slice preparation from neonatal rat that spontaneously generates respiratory rhythm, we patch-clamped inspiratory neurons in the preBötzinger complex (preBötC), the hypothesized site for respiratory rhythm generation, and simultaneously recorded respiratory-related motor output from the hypoglossal nerve (XIIn). Most (88%) of the inspiratory neurons tested responded to local application of acetylcholine (ACh) or carbachol (CCh) or bath application of muscarine. Bath application of 50 microM muscarine increased the frequency, amplitude, and duration of XIIn inspiratory bursts. At the cellular level, muscarine induced a tonic inward current, increased the duration, and decreased the amplitude of the phasic inspiratory inward currents in preBötC inspiratory neurons recorded under voltage clamp at -60 mV. Muscarine also induced seizure-like activity evident during expiratory periods in XIIn activity; these effects were blocked by atropine. In the presence of tetrodotoxin (TTX), local ejection of 2 mM CCh or ACh onto preBötC inspiratory neurons induced an inward current along with an increase in membrane conductance under voltage clamp and induced a depolarization under current clamp. This response was blocked by atropine in a concentration-dependent manner. Bath application of 1 microM pirenzepine, 10 microM gallamine, or 10 microM himbacine had little effect on the CCh-induced current, whereas 10 microM 4-diphenylacetoxy-N-methylpiperidine methiodide blocked the current. The current-voltage (I-V) relationship of the CCh-induced response was linear in the range of -110 to -20 mV and reversed at -11.4 mV. Similar responses were found in both pacemaker and nonpacemaker inspiratory neurons. The response to CCh was unaffected when patch electrodes contained a high concentration of EGTA (11 mM) or bis-(o-aminophenoxy)-N,N,N',N'-tetraacetic acid (10 mM). The response to CCh was reduced greatly by substitution of 128 mM Tris-Cl for NaCl in the bath solution; the I-V curve shifted to the left and the reversal potential shifted to -47 mV. Lowering extracellular Cl(-) concentration from 140 to 70 mM had no effect on the reversal potential. These results suggest that in preBötC inspiratory neurons, ACh acts on M3-like ACh receptors on the postsynaptic neurons to open a channel permeable to Na(+) and K(+) that is not Ca(2+) dependent. This inward cation current plays a major role in depolarizing preBötC inspiratory neurons, including pacemakers, that may account for the ACh-induced increase in the frequency of respiratory motor output observed at the systems/behavioral level.

Parametric survival analysis for gating kinetics of single potassium channels

The gating mechanism and the role of the S4 region in the activation of Shaker potassium channel was studied by statistical analysis on the wild type and mutant channels which have mutations in the S4 region. Single channel currents were recorded with the patch-clamp technique. The first latency time was analyzed with a parametric survival time regression model in which the generalized gamma distribution for the error term was assumed. Discrimination among Weibull, gamma, log-normal and exponential distributions was done with the likelihood ratio test. The three-parameter generalized gamma distribution was shown to be appropriate for the data set. The multiple regression function provides the statistical tests and the quantitative descriptions for the relationships between the mutations and the voltage dependence of the gating process. These results on statistical relations support the hypothesis that the S4 region plays an important role in sensing transmembrane voltage in the gating process, but the gating mechanism is not solely accounted for by the electrostatic interaction between the charged amino acids and the transmembrane voltage field. This work demonstrates that the survival analysis procedures can be useful tools for analyzing neurophysiological signals.

Respiratory rhythm generation and synaptic inhibition of expiratory neurons in pre-Bötzinger complex: differential roles of glycinergic and GABAergic neural transmission

A key distinction between neural pacemaker and conventional network models for the generation of breathing rhythm in mammals is whether phasic reciprocal inhibitory interactions between inspiratory and expiratory neurons are required. In medullary slices from neonatal rats generating respiratory-related rhythm, we measured the phasic inhibitory inputs to expiratory neurons with the use of whole cell patch clamp in the hypothesized rhythm generation site, the pre-Bötzinger complex (pre-BötC). Expiratory neurons, which generate tonic impulse activity during the expiratory period, exhibited inhibitory postsynaptic potentials (IPSPs) synchronized to the periodic inspiratory bursts of the hypoglossal nerve root (XIIn). Bath application of the glycine receptor antagonist strychnine (STR; 5-10 microM) reversibly blocked these inspiratory-phase IPSPs, whereas the gamma-aminobutyric acid-A (GABA(A)) receptor antagonist bicuculline (BIC; 10-100 microM) had no effect on these IPSPs. Replacing the control in vitro bathing solution with a Cl(-)-free solution also abolished these IPSPs. Respiratory-related rhythmic activity was not abolished when inspiratory-phase IPSPs were blocked. The frequency and strength of XIIn rhythmic activity increased and seizurelike activity was produced when either STR, BIC, or Cl(-)-free solution was applied. Inspiratory-phase IPSPs were stable after establishment of whole cell patch conditions (patch pipettes contained 7 mM Cl-). Under voltage clamp, the reversal potential of inspiratory-phase inhibitory postsynaptic currents (IPSCs) was -75 mV. The current-voltage (I-V) curve for IPSCs shifted to the right when extracellular Cl- concentration was reduced by 50% (70 mM) and the reversal potential was reduced to -60 mV, close to the new Cl- Nernst potential. In tetrodotoxin (0.5 microM) under voltage clamp (holding potential = -45 mV), local application of glycine (1 mM) over pre-BötC induced an outward current and an increase in membrane conductance in expiratory neurons. The effect was blocked by bath application of STR (0.8-1 microM). Local application of the GABA(A) receptor agonist 4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridin-3-ol (THIP, 1 mM) induced an outward current and an increase in membrane conductance that was blocked by BIC (10-100 mM). Under voltage clamp (holding potential = -45 mV), we analyzed spontaneous IPSCs during expiration in expiratory neurons. Bath application of BIC (10 microM) reduced the IPSC frequency (from 2.2 to 0.3 per s), whereas the inspiratory-phase IPSCs did not change. Bath application of STR (8-10 microM) abolished both IPSCs. These results indicate that 1) reciprocal inhibition of expiratory neurons is glycinergic and mediated by a glycine-activated Cl- channel that is not required for respiratory-related rhythm generation in neonatal rat medullary slices; 2) endogenous GABA and glycine modulate the excitability of respiratory neurons and affect respiratory pattern in the slice preparation; 3) both glycine and GABA(A) receptors are found on pre-BötC expiratory neurons, and these receptors are sensitive to STR and BIC, respectively; 4) glycine and GABA(A) inhibitory mechanisms play different functional roles in expiratory neurons: both glycine and GABA(A) receptors modulate neuronal excitability, whereas glycinergic transmission alone is responsible for reciprocal inhibition; and 5) intracellular Cl- concentration in these neonatal expiratory neurons is similar to that in adults.

Measure and statistical test for cross-correlation between paired neuronal spike trains with small sample size

Recent development of multi-unit recording techniques such as optical recording and multi-electrode arrays makes it possible to record neuronal activities from tens or hundreds of neurons simultaneously. To analyze functional connections between these neurons, cross-correlation analysis has been most commonly applied to the hundreds to thousands of pairs of these neurons. However, conventional cross-correlation data needs statistical tests for significance especially when the sample size of recorded spike trains is small. Here, a multiple hypergeometric model based on a transformation of the cross-correlogram data to a 2 x J table has been suggested. The exact p value for significance can be obtained by the generalized Fisher's method with small sample size and a cross-correlation coefficient for the strength of cross-correlation can be obtained based on the R-square analogue for nominal data. For large sample size, chi 2 test can be applied based on the same transformation. Examples of real spike train data set and simulation show that the methods are applicable to the data of multi-unit activity with only tens of spikes. These methods are especially useful when thousands of cross-correlograms need to be screened quickly and automatically.

Electrostatic interactions of S4 voltage sensor in Shaker K+ channel

The S4 segment comprises part of the voltage sensor in Shaker K+ channels. We have used a strategy similar to intragenic suppression, but without a genetic selection, to identify electrostatic interactions of the S4 segment that may be important in the mechanism of voltage-dependent activation. The S4 neutralization mutations K374Q and R377Q block maturation of the protein, suggesting that they prevent proper folding. K374Q is specifically and efficiently rescued by the second site mutations E293Q and D316N, located in putative transmembrane segments S2 and S3, respectively. These results suggest that K374, E293, and D316 form a network of strong, local, electrostatic interactions that stabilize the structure of the channel. Some other double mutant combinations result in inefficient suppression, identifying weak, presumably long-range electrostatic interactions. A simple structural hypothesis is proposed to account for the effects of the rescued double mutant combinations on the relative stabilities of open and closed channel conformations.

Computed tomography in predicting the efficacy of oral cholelitholysis with bile acids

The efficacy of oral cholelitholytic therapy with chenodeoxycholic acid (CDCA) and ursodeoxycholic acid (UDCA) in 137 patients with gallstones was studied in relation to their CT patterns. The best dissolving results were obtained in patients with the stones in isodensity and faint category (< 50 Hu) on CT. The stones with high density or heterogeneous calcification on CT were insoluble, and therefore, were contraindicated for oral cholelitholytic therapy. The attenuation value of stones was classified as complete dissolution ranged from -2 to 35 Hu (14 +/- 12 Hu, n = 13), and their upper limit of 95 percentiles was 33.4 Hu. CT analysis improved the predictability of dissolving gallstones in comparison with plain abdominal radiography or oral cholecystography (OCG). The complete dissolving rate increased from 9.49% (13/137) in patients selected by classic X-ray to 40.7% (11/27) in isodensity category on CT. Besides, radiolucent gallstones, which showed no obvious filling defect on OCG but distinct echo and shadow on B-type ultrasonography, were also insoluble.

S4 mutations alter the single-channel gating kinetics of Shaker K+ channels

The S4 sequence comprises at least part of the voltage sensor in Shaker K+ channels. Two site-directed mutations in the Shaker S4 sequence, R368Q and R377K, which decrease the voltage dependence of the whole-cell current, alter voltage-dependent gating at the single-channel level. Compared with the wild-type channel, they increase the latency to first opening, destabilize the open state, and alter the equilibria of voltage-dependent transitions, so that some of the charge movement occurs after the first opening. Whether these changes reflect a new mechanism of activation is a key question. Although the mutations alter the kinetics of many steps in the gating process, we conclude that the mutant channels are likely to activate using the same fundamental mechanism as wild-type channels.

[Pathological changes in adrenal cortex in rats after phosphorus burn (stereological and histochemical changes)]

The experiment dealt with stereological and histochemical study on the submicroscopic structure of adrenal cortex after phosphorus burn within 15 days. The main findings were as follows: (1). The increased dense lysosome-like bodies in the adrenal cortical cells after burn were not all lysosomes, and it was conjectured they were hormone carrier-protein which might come from the Golgi complex; (2). The ZR cells developed better and had more abundant organelles and higher enzymic activity than other zonal cells. These differences were more obvious after burn. We speculated that ZR was not a degenerated zone, but an important functional area of synthesis and secretion of steroid hormone; (3) Different cellular functional conditions in adrenal cortex were related to the secretory rhythm of the cells.

Activation and desensitization of the 5-HT3 receptor in a rat glioma x mouse neuroblastoma hybrid cell

1. Tight-seal voltage-clamp techniques were used to study the 5-HT3 receptor of differentiated NG108-15 cells. 2. The inward current caused by 5-HT was dependent on the 5-HT concentration: the apparent dissociation constant was 3.3 microM and the Hill coefficient was 1.8. 3. Immediately after establishing a recording, sustained application of a saturating concentration of 5-HT caused the response to decline with a half-time of 0.57 s (at a membrane potential of -70 mV). The time course of desensitization was best fitted by a sum of two exponentials. 4. Desensitization became slower during the first 10 min of recording in the whole-cell configuration, with the half-time for response decay increasing to 1.8 s. The deceleration of desensitization may result from wash-out of a cytoplasmic regulator of the receptor. 5. Desensitization declined less during whole-cell recordings when patch pipettes contained non-hydrolysable analogues of adenosine 5'-triphosphate. 6. Desensitization developed more rapidly following the addition of forskolin, prostaglandin E1, cholera toxin or 1,9-dideoxyforskolin to the recording medium. Non-hydrolysable adenosine 5'-phosphate analogues had no effect on the enhancement of desensitization induced by forskolin.

Differentiation of NG108-15 cells alters channel conductance and desensitization kinetics of the 5-HT3 receptor

1. NG108-15 cells undergo morphological differentiation in response to appropriate culture conditions. We have used patch clamp techniques to compare responses mediated by the 5-HT3 receptor in differentiated and undifferentiated NG108-15 cells. 2. In differentiated cells, desensitization of 5-hydroxytryptamine (5-HT) responses was much slower than in undifferentiated cells. Desensitization in differentiated cells was also highly variable, with half-times varying by greater than 40-fold. Rapidly desensitized responses in differentiated cells were qualitatively similar to the responses of undifferentiated cells. 3. In outside-out patches from undifferentiated cells, single channel currents could be seen after 5-HT application. These channels had a conductance of 12 pS. The 5-HT-activated channels in differentiated cells were too small to observe at the single-channel level. Noise analysis indicated that the channel conductance was approximately 4 pS. In differentiated cells, both rapidly and slowly desensitized responses were generated by channels with essentially the same conductance. 4. The 5-HT responses of differentiated cells were also distinguished from those of undifferentiated cells on the basis of the voltage dependence of desensitization and the curvature of the current-voltage curve. 5. NG108-15 cells can produce different receptor subtypes, which may be expressed in different tissues or at different stages of development. These variations in receptor behavior suggest that there are at least two distinct mechanisms for regulation of the 5-HT3 receptor.

[An experimental study on pathological changes in adrenal cortex in rats after phosphorus burn. I. Ultrastructural changes]

We observed the ultrastructural (PCC) changes in the adrenal zona fasciculata (ZF) and zona reticularis (ZR) and plasma corticosterone levels after phosphorus burn in rats within 15 days. We found that the PCC in the burnt rats increased remarkably with 3 peaks, and all the organelles or the surface structures (filopodia and cytoplasmic processes) in ZF and ZR cells showed various changes, which we considered as variant forms of secretion and synthesis hyperfunction of the adrenal cortical cells. There were also degenerative changes in the membrane structure.

The selectivity of the channel coupled to the 5-HT3 receptor

The 5-HT3 receptor is unusual among receptors for biogenic amines in that it is directly coupled to an ion channel that is highly permeable to Na+ and K+. We have studied the permeation properties of this channel in order to achieve a more detailed understanding of its physiological function and to extend the comparison with other ligand gated channels. The 5-HT3 receptor channel is significantly permeable to the organic cations Tris, choline, and N-methyl-glucamine, with permeabilities decreasing with size. The permeability ratios for Tris and choline are similar to those determined for the nicotinic receptor; the permeability ratio for Tris is also similar to that of a non-N-methyl-D-aspartate (non-NMDA) excitatory amino acid receptor. This suggests that the diameters at the narrowest parts of these 3 channels are similar. The Ca2+ permeability of the 5-HT3 receptor channel is relatively low, with an upper bound to PCa/PNa estimated as 0.076. The single channel conductance, as determined by noise analysis, was also relatively low, with a value of 4.4 +/- 0.5 pS. Thus, both the Ca2+ permeability and single channel conductance are lower than those of the nicotinic receptor. In these respects, the 5-HT3 receptor is closer to non-NMDA excitatory amino acid receptors. These results are interpreted in terms of a model of the 5-HT3 receptor channel in which the interior has a lower polarizability, and possibly a greater length, in comparison with the nicotinic acetylcholine receptor channel.

Treatment of hyaline membrane disease by human amniotic fluid surfactant

A case of hyaline membrane disease was treated successfully with pulmonary surfactant (PS) isolated from human amniotic fluid. Dosage was 150 mg phospholipid/kg. The exogenous surfactant was instilled into the airway via a tracheal cannula. Clinical symptoms, PO2 and FiO2 improved evidently 24 hours after administration. L/S ratio and phosphatidylglycerol recovered gradually in aspirates. Lung X-ray film manifested "white lung" before instillation of surfactant and showed a striking improvement 3 days after treatment. The duration of mechanical ventilation was 6 days. During the period of recovery complications of patent ductus arteriosus and bacterial pneumonia developed. However, the patient recovered completely and was discharged 32 days after admission.