The plasma peptides of sepsis

Background

A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast cancer, female normal, sepsis, heart attack, Alzheimer’s and multiple sclerosis along with their institution-matched controls, female normals and normal samples collected directly onto ice.

Methods

Endogenous tryptic peptides were extracted from individual sepsis and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The protein observation frequency of ICU-sepsis versus ICU Control was subsequently tested by Chi square analysis. The average protein or peptide log₁₀ precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system.

Results

Peptides and/or phosphopeptides of common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 showed increased observation frequency by Chi square (χ² > 9, p < 0.003) and/or precursor intensity in sepsis. Cellular gene symbols with large Chi square values from tryptic peptides included POTEB, CTNNA1, U2SURP, KIF24, NLGN2, KSR1, GTF2H1, KIT, RPS6KL1, VAV2, HSPA7, SMC2, TCEB3B, ZNF300, SUPV3L1, ADAMTS20, LAMB4, MCCC1, SUPT6H, SCN9A, SBNO1, EPHA1, ABLIM2, cB5E3.2, EPHA10, GRIN2B, HIVEP2, CCL16, TKT, LRP2 and TMF1 amongst others showed increased observation frequency. Similarly, increased frequency of tryptic phosphopeptides were observed from POM121C, SCN8A, TMED8, NSUN7, SLX4, MADD, DNLZ, PDE3B, UTY, DEPDC7, MTX1, MYO1E, RXRB, SYDE1, FN1, PUS7L, FYCO1, USP26, ACAP2, AHI1, KSR2, LMAN1, ZNF280D and SLC8A2 amongst others. Increases in mean precursor intensity in peptides from common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 as well as cellular proteins such as COL24A1, POTEB, KANK1, SDCBP2, DNAH11, ADAMTS7, MLLT1, TTC21A, TSHR, SLX4, MTCH1, and PUS7L among others were associated with sepsis. The processing of SAA1 included the cleavage of the terminal peptide D/PNHFRPAGLPEKY from the most hydrophilic point of SAA1 on the COOH side of the cystatin C binding that was most apparent in ICU-Sepsis patients compared to all other diseases and controls. Additional cleavage of SAA1 on the NH2 terminus side of the cystatin binding site were observed in ICU-Sepsis. Thus there was disease associated variation in the processing of SAA1 in ICU-Sepsis versus ICU controls or other diseases and controls.

Conclusion

Specific proteins and peptides that vary between diseases might be discovered by the random and independent sampling of multiple disease and control plasma from different hospital and clinics by LC–ESI–MS/MS for storage in a relational SQL Server database and analysis with the R statistical system that will be a powerful tool for clinical research. The processing of SAA1 may play an unappreciated role in the inflammatory response to Sepsis.

The plasma peptides of breast versus ovarian cancer

Background

There is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous tryptic peptides of breast cancer plasma were compared to ovarian cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with the institution-matched normal and control samples collected directly onto ice.

Methods

Endogenous tryptic peptides were extracted from individual breast cancer and control EDTA plasma samples in a step gradient of acetonitrile, and collected over preparative C18 for LC-ESI-MS/MS with a set of LTQ XL linear quadrupole ion traps working together in parallel to randomly and independently sample clinical populations. The MS/MS spectra were fit to fully tryptic peptides or phosphopeptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The observation frequency was subsequently tested by Chi Square analysis. The log₁₀ precursor intensity was compared by ANOVA in the R statistical system.

Results

Peptides and/or phosphopeptides of common plasma proteins such as APOE, C4A, C4B, C3, APOA1, APOC2, APOC4, ITIH3 and ITIH4 showed increased observation frequency and/or precursor intensity in breast cancer. Many cellular proteins also showed large changes in frequency by Chi Square (χ² > 100, p < 0.0001) in the breast cancer samples such as CPEB1, LTBP4, HIF-1A, IGHE, RAB44, NEFM, C19orf82, SLC35B1, 1D12A, C8orf34, HIF1A, OCLN, EYA1, HLA-DRB1, LARS, PTPDC1, WWC1, ZNF562, PTMA, MGAT1, NDUFA1, NOGOC, OR1E1, OR1E2, CFI, HSA12, GCSH, ELTD1, TBX15, NR2C2, FLJ00045, PDLIM1, GALNT9, ASH2L, PPFIBP1, LRRC4B, SLCO3A1, BHMT2, CS, FAM188B2, LGALS7, SAT2, SFRS8, SLC22A12, WNT9B, SLC2A4, ZNF101, WT1, CCDC47, ERLIN1, SPFH1, EID2, THOC1, DDX47, MREG, PTPRE, EMILIN1, DKFZp779G1236 and MAP3K8 among others. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. An increase in mean precursor intensity of peptides was observed for QSER1 as well as SLC35B1, IQCJ-SCHIP1, MREG, BHMT2, LGALS7, THOC1, ANXA4, DHDDS, SAT2, PTMA and FYCO1 among others. In contrast, the QSER1 peptide QPKVKAEPPPK was apparently specific to ovarian cancer.

Conclusion

There was striking agreement between the breast cancer plasma peptides and proteins discovered by LC-ESI-MS/MS with previous biomarkers from tumors, cells lines or body fluids by genetic or biochemical methods. The results indicate that variation in plasma peptides from breast cancer versus ovarian cancer may be directly discovered by LC-ESI-MS/MS that will be a powerful tool for clinical research. It may be possible to use a battery of sensitive and robust linear quadrupole ion traps for random and independent sampling of plasma from a multisite clinical trial.

The plasma peptides of ovarian cancer

Background

It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma by using liquid chromatography and tandem mass spectrometry to identify, quantify and compare the peptides cleaved ex vivo from different clinical populations. The endogenous tryptic peptides of ovarian cancer plasma were compared to breast cancer and female cancer normal controls, other diseases with their matched or normal controls, plus ice cold plasma to control for pre-analytical variation.

Methods

The endogenous tryptic peptides or tryptic phospho peptides (i.e. without exogenous digestion) were analyzed from 200 μl of EDTA plasma. The plasma peptides were extracted by a step gradient of organic/water with differential centrifugation, dried, and collected over C18 for analytical HPLC nano electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) with a linear quadrupole ion trap. The endogenous peptides of ovarian cancer were compared to multiple disease and normal samples from different institutions alongside ice cold controls. Peptides were randomly and independently sampled by LC–ESI–MS/MS. Precursor ions from peptides > E4 counts were identified by the SEQUEST and X!TANDEM algorithms, filtered in SQL Server, before testing of frequency counts by Chi Square (χ²), for analysis with the STRING algorithm, and comparison of precursor intensity by ANOVA in the R statistical system with the Tukey-Kramer Honestly Significant Difference (HSD) test.

Results

Peptides and/or phosphopeptides of common plasma proteins such as HPR, HP, HPX, and SERPINA1 showed increased observation frequency and/or precursor intensity in ovarian cancer. Many cellular proteins showed large changes in frequency by Chi Square (χ² > 60, p < 0.0001) in the ovarian cancer samples such as ZNF91, ZNF254, F13A1, LOC102723511, ZNF253, QSER1, P4HA1, GPC6, LMNB2, PYGB, NBR1, CCNI2, LOC101930455, TRPM5, IGSF1, ITGB1, CHD6, SIRT1, NEFM, SKOR2, SUPT20HL1, PLCE1, CCDC148, CPSF3, MORN3, NMI, XTP11, LOC101927572, SMC5, SEMA6B, LOXL3, SEZ6L2, and DHCR24. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. Analysis of the frequently observed proteins by ANOVA confirmed increases in mean precursor intensity in ZFN91, TRPM5, SIRT1, CHD6, RIMS1, LOC101930455 (XP_005275896), CCDC37 and GIMAP4 between ovarian cancer versus normal female and other diseases or controls by the Tukey–Kramer HSD test.

Conclusion

Here we show that separation of endogenous peptides with a step gradient of organic/water and differential centrifugation followed by random and independent sampling by LC–ESI–MS/MS with analysis of peptide frequency and intensity by SQL Server and R revealed significant difference in the ex vivo cleavage of peptides between ovarian cancer and other clinical treatments. There was striking agreement between the proteins discovered from cancer plasma versus previous biomarkers discovered in tumors by genetic or biochemical methods. The results indicate that variation in plasma proteins from ovarian cancer may be directly discovered by LC–ESI–MS/MS that will be a powerful tool for clinical research.

Electronic supplementary material

The online version of this article (10.1186/s12014-018-9215-z) contains supplementary material, which is available to authorized users.

The plasma peptidome

Background

It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma using LC–ESI–MS/MS to identify, with a linear quadrupole ion trap to identify, quantify and compare the statistical distributions of peptides cleaved ex vivo from plasma samples from different clinical populations.

Methods

A systematic method for the organic fractionation of plasma peptides was applied to identify and quantify the endogenous tryptic peptides from human plasma from multiple institutions by C18 HPLC followed nano electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) with a linear quadrupole ion trap. The endogenous tryptic peptides, or tryptic phospho peptides (i.e. without exogenous digestion), were extracted in a mixture of organic solvent and water, dried and collected by preparative C18. The tryptic peptides from 6 institutions with 12 different disease and normal EDTA plasma populations, alongside ice cold controls for pre-analytical variation, were characterized by mass spectrometry. Each patient plasma was precipitated in 90% acetonitrile and the endogenous tryptic peptides extracted by a stepwise gradient of increasing water and then formic acid resulting in 10 sub-fractions. The fractionated peptides were manually collected over preparative C18 and injected for 1508 LC–ESI–MS/MS experiments analyzed in SQL Server R.

Results

Peptides that were cleaved in human plasma by a tryptic activity ex vivo provided convenient and sensitive access to most human proteins in plasma that show differences in the frequency or intensity of proteins observed across populations that may have clinical significance. Combination of step wise organic extraction of 200 μL of plasma with nano electrospray resulted in the confident identification and quantification ~ 14,000 gene symbols by X!TANDEM that is the largest number of blood proteins identified to date and shows that you can monitor the ex vivo proteolysis of most human proteins, including interleukins, from blood. A total of 15,968,550 MS/MS spectra ≥ E4 intensity counts were correlated by the SEQUEST and X!TANDEM algorithms to a federated library of 157,478 protein sequences that were filtered for best charge state (2+ or 3+) and peptide sequence in SQL Server resulting in 1,916,672 distinct best-fit peptide correlations for analysis with the R statistical system. SEQUEST identified some 140,054 protein accessions, or some ~ 26,000 gene symbols, proteins or loci, with at least 5 independent correlations. The X!TANDEM algorithm made at least 5 best fit correlations to more than 14,000 protein gene symbols with p-values and FDR corrected q-values of ~ 0.001 or less. Log₁₀ peptide intensity values showed a Gaussian distribution from E8 to E4 arbitrary counts by quantile plot, and significant variation in average precursor intensity across the disease and controls treatments by ANOVA with means compared by the Tukey–Kramer test. STRING analysis of the top 2000 gene symbols showed a tight association of cellular proteins that were apparently present in the plasma as protein complexes with related cellular components, molecular functions and biological processes.

Conclusions

The random and independent sampling of pre-fractionated blood peptides by LC-ESI-MS/MS with SQL Server-R analysis revealed the largest plasma proteome to date and was a practical method to quantify and compare the frequency or log₁₀ intensity of individual proteins cleaved ex vivo across populations of plasma samples from multiple clinical locations to discover treatment-specific variation using classical statistics suitable for clinical science. It was possible to identify and quantify nearly all human proteins from EDTA plasma and compare the results of thousands of LC–ESI–MS/MS experiments from multiple clinical populations using standard database methods in SQL Server and classical statistical strategies in the R data analysis system.

Electronic supplementary material

The online version of this article (10.1186/s12014-018-9211-3) contains supplementary material, which is available to authorized users.

A method for the extraction of the endogenous tryptic peptides (peptidome) from human EDTA plasma

The proteins identified from endogenous peptides agreed between serum versus plasma, and tryptic versus non-tryptic peptides, when collected by C18 alone and analyzed by liquid chromatography electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) including amyloids, apolipoproteins, haptoglobin, complements, fibrinogens, hemopexin, antitrypsin and alpha 2 macroglobulin. Precipitation of polypeptides from plasma in 9 vol of 100% organic solvent followed by stepwise extraction of the insoluble pellet with an increasing fraction of water identified thousands of proteins. A Coomassie-blue protein binding assay, and tricine SDS-PAGE, showed that Acetonitrile-Water (AH) resulted in a greater relative enrichment of low molecular weight plasma polypeptides than Acetonitrile-Methanol Water (AMH). A total of 905,386 MS/MS spectra greater than ~10,000 (E4) counts were correlated by X!TANDEM to a federated human protein library of 153,124 different protein sequences that resulted in 58,223 fully tryptic peptides from 3463 Gene Symbols of which 1880 had ≥ 5 independent peptides (p ≤ 0.00001). The results were filtered and organized in an SQL database for analysis using the generic R statistical analysis system. Cellular proteins including secreted and exosome proteins, signaling factors, nucleic acid binding proteins, metabolic enzymes and uncharacterized factors were observed with a significant enrichment of expected protein-protein interactions by STRING analysis.

Managing waiting time for radiotherapy: A single machine unit experience

Waiting time (WT) for radiotherapy (RT) is a significant clinical problem. This paper examines various strategies for managing WT for patients treated with radical and palliative intent in the new setting of a rural single machine unit in Australia. Cohorts of patients undergoing both radical and palliative RT in Bendigo had their WT prospectively recorded. Matched cohorts from the hub centre (Peter MacCallum Cancer Centre, Melbourne) treated with palliative intent were also collated. Strategies implemented included a devoted priority meeting, palliative points system, and reallocation of appointment times. The audit was to continue until best practice guidelines were bettered. Three cohorts of patients were compared. There is a significant trend for increasing numbers of patients treated per month since the centre opened (P < 0.0001). The ratio of palliative to radical intent patients remained stable between 46 and 52%. Mean WT for palliative RT reduced from 25 days in the first cohort to 7 days in the final cohort (P < 0.0005). Waiting time for palliative RT was initially longer at Bendigo than the hub centre (P < 0.0005), but by the final cohort there was a non-significant difference favouring the Bendigo cohort (P = 0.26). Waiting time for radical treatment also improved throughout the three cohorts in Bendigo (P < 0.0005). A number of new strategies have successfully resulted in the abolition of lengthy WT for RT in Bendigo despite the increasing demand for the RT service.

Keratins of the human hair follicle: "hyperproliferative" keratins consistently expressed in outer root sheath cells in vivo and in vitro

Keratins produced by morphologically distinct compartments of the human hair folicle (hHF) were analysed and compared to those produced by cultured hHF and interfollicular keratinocytes. Five of the major keratins, the basic keratins nos. 5 and 6 (apparent mol. mass 60 and 58 kDa) and the acidic keratins nos. 14, 16, and 17 (51, 49 and 48 kDa), could be labelled in intact hHF and were found in all fractions of the outer root sheath (ORS). The other major keratins, which were not labelled under these conditions (basic-neutral hHbI and -II; 60-62 kDa and acidic hHaI and -II; 40-42 kDa) were associated with hair shaft (hHS) both in the follicle and, virtually unchanged, in the distal part of the hair. Another, previously undescribed, group of proteins with keratin-like properties exhibiting a broad pI-spectrum (basic to slightly acidic: hIC-I, -II, -III, 64-67 kDa; distinctly acidic: hIC-IV, about 54 kDa) was detected in isolated inner root sheath (IRS), in the cuticular material shed from denuded hHS, and also in nail plates. In our experiments only ORS cells grew readily in culture irrespective of their origin from peripheral (mesenchyme-adjacent) or more central ORS-cell layers. In contrast to keratinocytes from interfollicular epidermis (IFE) the cultured ORS cells expressed a keratin set virtually identical to that expressed in vivo. This set also closely resembled that expressed by IFE keratinocyte cultures. The identity of the respective keratins (nos. 5, 6, 14, 16, and 17) present in all these cells in vivo and in vitro was confirmed by tryptic peptide mapping. The data indicated that the microenvironment (in situ) directs the differentiation of ORS cells in a manner comparable to the way it is directed by conventional culture conditions, with consistent expression of the "basal" and "hyperproliferative" set of keratins. This, however, does not exclude the possibility that other types of environmentally induced response may occur, as seen for example during the reepithelialization of superficial skin wounds by ORS cells.

Treatment and justice

Support for the belief that criminal behaviour was amenable to treatment served different purposes: for developing psychiatry it offered a module of power to be exploited whereas for the State it was a convenient disguise for the infliction of pain which was the real intention of punishment. Having served its purpose the treatment approach is being abandoned in favour of a philosophy of just deserts which is more acceptable in the present political climate.

What happens to patients released from the special hospitals?

NHS consultants who are asked to accept Special Hospital patients can judge the prognosis, since the extent of both psychiatric and criminal histories provides the most accurate prediction of future behaviour. Patients discharged to the community have different outcomes from those transferred to NHS hospitals, but overall about one in five of those released are returned to a Special Hospital; up to one in two will subsequently be convicted, but the offences are mainly trivial and directed at property. Perhaps one in ten will be involved in serious or homicidal acts of violence.

A psychiatric clinic in a probation office

A weekly clinic was held for one year in a London probation office with 41 probation officers. Only 23 cases were referred but the clinic was found to be a valuable forum for discussion of problems with the officers, 10 per cent of whose clients were estimated to be receiving psychiatric treatment elsewhere. Suggestions are made to improve collaboration between psychiatrists and probation officers.

Men remanded into custody for medical reports: the selection for treatment

In a sample of men remanded into custody for medical reports during a three-month period, it was found that those who received recommendations for treatment had a diagnosis of acute mental illness, had in the past been admitted more frequently to mental hospitals and had spent a longer period as in-patients. They were also assessed as being difficult to manage, i.e. they were considered to be nuisances, were threatening and potentially violent. The men who were not recommended for treatment had a history of excessive drinking and drink-related offences; they also had more extensive criminal histories and a diagnosis of psychopathic disorder.

Men remanded into custody for medical reports: the outcome of the treatment recommendation

Over a three-month period, 634 men were remanded into custody at Brixton Prison for medical reports; 87 received recommendations for psychiatric treatment and 82 individuals were actually referred to hospitals for treatment. Fourteen months later nearly three-quarters of the men who went to hospital had been discharged. They fell into three groups by outcome: men with acute psychoses for whom treatment was definitely beneficial; men who remained behaviourally disturbed after receiving treatment although their mental states improved; a group with chronic disorders for whom admission was not beneficial. The two groups with improved mental states represented only 5 per cent of the initial receptions to Brixton Prison.

The NHS practice of forensic psychiatry in one region

The present paper outlines the number and distribution of forensic patients within one region. In addition, attitudes to both available services and existing legislation are described. Regional and national data are compared so that the results can be used by other regions which are currently planning a development of their own forensic services.

Medical practice: defendants and prisoners

It is argued in this paper that a doctor cannot serve two masters. The work of the prison medical officer is examined and it is shown that his dual allegiance to the state and to those individuals who are under his care results in activities which largely favour the former. The World Health Organisation prescribes a system of health ethics which indicates, in qualitative terms, the responsibility of each state for health provisions. In contrast, the World Medical Association acts as both promulgator and guardian of a code of medical ethics which determines the responsibilities of the doctor to his patient. In the historical sense medical practitioners have always emphasized the sanctity of the relationship with their patients and the doctor's role as an expert witness is shown to have centered around this bond. The development of medical services in prisons has focused more on the partnership between doctor and institution. Imprisonment in itself could be seen as prejudicial to health as are disciplinary methods which are more obviously detrimental. The involvement of medical practitioners in such procedures is discussed in the light of their role as the prisoner's personal physician.

The relationship between different evaluations of drinking behaviour

Prisoners' attitudes to their drinking behaviour, although largely accurate, minimize problems in terms of other assessments made at interview. Semantic differences are apparent in the use of the terms 'heavy' and 'problem' as descriptions of drinking behaviour; thus men who admit heavy but deny problem drinking are often reported to be problem drinkers by their family and myself. There is close agreement between the family's reported attitude to a man's drinking and the assessment made in a structured psychiatric interview.

Liberty and psychiatry

The security facilities available in one regional health authority area have been surveyed. The simultaneous run-down of the large mental hospitals and the open-door policy have resulted in a lack of facilities for mentally abnormal offenders, and the increasing scarcity of common lodging houses has exacerbated the problem. Newer psychiatric units associated with general hospitals have been mainly concerned with patients suffering from neurosis or acute psychoses. The failure to develop other services to deal with offenders has seriously overburdened both the penal system and the special hospitals.

Reliability of prisoners' attitudes to their drinking behaviour

A sample of male prisoners was examined by means of a questionnaire and subsequently by a structured interview. Control subjects who denied heavy drinking were used to study test-retest reliability of a group who admitted that drinking was a problem and a third group who admitted heavy drinking but denied problem drinking. Non-heavy drinkers and the heaviest drinkers are shown to be the most reliable and the intermediate group least reliable.

Smoking and optic neuritis

The effect of smoking on the recovery of visual function after an attack of optic neuritis has been assessed in 125 patients. Heavy smokers were found to have a higher incidence of red/green colour vision defects than non-smokers. The possible implications of this finding are discussed.

One patient is described in whom smoking caused transient blurring of vision. The effects of nicotine on the central nervous system are reviewed, and a pathophysiological mechanism suggested for this phenomenon.

The psychiatric aspects of cardiac intensive therapy: a review

The post cardiotomy state is typically delirious and although organic factors are important it is multi-determined. Cerebral ischaemia has been implicated in the development of psychological disorder after resuscitation but longer term neurotic disorders also occur. Affective disturbances, particularly depression, are associated with the coronary care experience. The following conditions are directly related to an increased incidence of psychological disorder: age, loss of sleep, sensory deprivation, stressful experiences, pre-operative morbidity (both physical and mental), the severity of both surgical trauma and the post-operative medical state. For both the staff who administer intensive therapy and the patient who receives it there are unique psychological hazards, the management of which depends largely on mutual understanding and support.