PeptideXme Patient Report

pX_0001
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Patient
HCC-2025-0042
Diagnosis
Hepatocellular Carcinoma (HCC)
Stage
Stage IIIB (BCLC C)
Report Date
2025-09-04
Institution
Lund University — HCC Translational Lab
Turnaround
26 days
Cover & Patient Summary
Executive Summary
Genomic Profile
Epigenetic Profile
Transcriptomic Profile
HLA Typing & Immunopeptidome
Neoantigen Candidates
Immune Profile & TME
Therapeutic Recommendations
Technical Appendix

Patient Summary

Report IDpX_0001
Patient PseudonymHCC-2025-0042
DiagnosisHepatocellular Carcinoma (HCC)
StageStage IIIB (BCLC C)
Sample TypeFFPE tumor tissue + matched blood
Date Received2025-07-20
Date Processed2025-08-15

Treatment History

  • Surgical resection (2024-03-15)
  • Transarterial chemoembolization (TACE) x2 (2024-06, 2024-08)
  • Currently on atezolizumab + bevacizumab (started 2025-01)

Sequencing Platforms

Illumina NovaSeq 6000 (WES) PacBio Revio (Iso-Seq) LC-MS/MS (immunopeptidomics) 10x Chromium (scRNA-seq)
147
Total Candidates
72
AS-Derived
38
Mutation-Derived
12
Fusion-Derived
10
MS-Validated

Top Neoantigen Candidate

PeptideSLADTNSL
SourceAlternative splicing (SE event in TTN)
HLA AlleleHLA-A*02:01
Binding Affinity (IC50)23.4 nM
Binding Rank0.12%
Immunogenicity Score0.87
MS ValidatedYes

TME Classification

Immune-excluded

TMB: 4.2 muts/Mb (Low)

MSI: MSS (Microsatellite Stable)

HLA Types

HLA-A*02:01 HLA-A*24:02 HLA-B*07:02 HLA-B*44:03 HLA-C*05:01 HLA-C*16:01

Top Recommendation

Personalized peptide vaccine targeting top 15 AS-derived neoepitopes + anti-PD-L1 combination

Neoantigen Source Distribution
52
Total Mutations
38
Coding Mutations
7
Driver Mutations
4.2
TMB (muts/Mb)

Somatic Mutations

GeneVariantVAFConsequenceClinical SignificanceDriver
TP53 c.733C>T (p.R248W) 34.0% Missense Pathogenic — dominant negative Driver
CTNNB1 c.110T>C (p.S37P) 28.0% Missense Pathogenic — Wnt pathway activation Driver
TERT c.-124C>T (promoter) 41.0% Promoter mutation Pathogenic — telomerase reactivation Driver
AXIN1 c.1582C>T (p.R528* 19.0% Nonsense Likely pathogenic — Wnt pathway Driver
ARID1A c.4891_4892del (p.G1631fs) 22.0% Frameshift Likely pathogenic — chromatin remodeling Driver
ARID2 c.2386C>T (p.Q796*) 16.0% Nonsense Likely pathogenic — chromatin remodeling Passenger
KEAP1 c.607C>T (p.R203*) 31.0% Nonsense Pathogenic — oxidative stress response Driver
NFE2L2 c.91_92insA (p.E31fs) 18.0% Frameshift Likely pathogenic — NRF2 activation Passenger
TSC2 c.1456C>T (p.R486*) 12.0% Nonsense VUS Passenger
VHL c.250C>T (p.P84S) 8.0% Missense VUS Passenger

Copy Number Alterations

GeneTypeCopy NumberLog2 Ratio
MYC Amplification 8 2.1
CCND1 Amplification 6 1.5
CDKN2A/B Homozygous deletion 0 -3.2
PTEN Heterozygous loss 1 -0.9
FGF19 Amplification 5 1.3
Mutation Spectrum

Global Methylation

Status: Global hypomethylation

Global score: 0.62

Hypermethylated regions: 1247 | Hypomethylated regions: 3892

Key Differentially Methylated Regions

GeneChangeFold ChangeSignificance
RASSF1A Hypermethylated 4.2x Tumor suppressor silencing
CDKN2A Hypermethylated 3.8x Cell cycle checkpoint loss
GSTP1 Hypermethylated 5.1x Detoxification pathway loss
APC Hypermethylated 2.9x Wnt pathway dysregulation

Splice-Regulatory Factor Expression

GeneMutationExpression (log2FC)Note
SF3B1 None detected 1.2 Upregulated — may drive aberrant splicing
U2AF1 None detected 0.8 Mildly upregulated
SRSF2 None detected 1.5 Upregulated — correlated with AS-derived neoepitope burden
HNRNPA2B1 None detected 2.1 Strongly upregulated
RBFOX2 None detected -1.3 Downregulated — loss of splicing fidelity
Splice-Regulatory Factor Expression (log2 Fold Change)
1284
Total AS Events
342
Tumor-Specific AS
72
Peptide-Generating
8
Fusions Detected

Top Alternative Splicing Events (Peptide-Generating)

IDTypeGenePSI (Tumor)PSI (Normal)Tumor-Specificity
AS_001 SE (Skipped Exon) TTN 0.12 0.89 0.95
AS_002 SE (Skipped Exon) MAGI2 0.08 0.92 0.91
AS_003 A3SS (Alt 3' Splice Site) FHIT 0.78 0.15 0.88
AS_004 RI (Retained Intron) DAB2 0.65 0.05 0.93
AS_005 MXE (Mutually Exclusive Exons) PKM 0.82 0.22 0.86
AS_006 SE (Skipped Exon) KIF1B 0.15 0.85 0.89
AS_007 A5SS (Alt 5' Splice Site) MACF1 0.72 0.18 0.87
AS_008 RI (Retained Intron) USP47 0.58 0.08 0.92
AS_009 SE (Skipped Exon) FAT1 0.2 0.88 0.9
AS_010 MXE (Mutually Exclusive Exons) CALD1 0.75 0.25 0.85

Gene Fusions

ID5' Partner3' PartnerReadsFrameTPMPeptide
FUS_001 DNAJB1 PRKACA 847 In-frame 156.3 Yes
FUS_002 TFEB CLTC 312 In-frame 42.7 Yes
FUS_003 ALK EML4 89 Out-of-frame 12.1 No
AS Event Type Distribution

HLA Class I Typing (4-digit resolution)

LocusAlleleConfidenceLOH
HLA-A A*02:01 0.99 Normal
HLA-A A*24:02 0.98 Normal
HLA-B B*07:02 0.99 LOH Detected
HLA-B B*44:03 0.97 Normal
HLA-C C*05:01 0.98 Normal
HLA-C C*16:01 0.96 Normal

HLA-B*07:02 shows loss of heterozygosity (LOH) in tumor — may impair antigen presentation on this allele

Immunopeptidome Summary

8421
Total Peptides (MS)
10
MS-Validated Neoantigens
9
Median Length (aa)
Immunopeptidome Source Distribution
147
Total Candidates
23
High Confidence
10
MS-Validated

7a: Mutation-Derived Neoantigens

RankPeptideGeneHLAIC50 (nM)Rank %Imm. ScoreTCR ProbMSTPMClonality
1 KLDKVNSL TP53 HLA-A*02:01 45.2 0.15 0.82 0.71 - 89.3 Trunk
2 STLPGVIAA CTNNB1 HLA-A*24:02 78.3 0.32 0.74 0.58 - 156.7 Trunk
3 RMPGSPAA KEAP1 HLA-B*07:02 112.5 0.45 0.68 0.52 - 234.1 Trunk
4 VTLNDEAA ARID1A HLA-A*02:01 234.8 0.89 0.61 0.43 - 45.2 Subclonal
5 YLDPSLTA AXIN1 HLA-B*44:03 189.3 0.72 0.65 0.47 - 67.8 Trunk

7b: Alternative Splicing-Derived Neoepitopes PeptideXme Differentiator

RankPeptideSourceGeneHLAIC50 (nM)Rank %Imm. ScoreTCR ProbMSTPMClonality
1 SLADTNSL AS-derived (SE) TTN HLA-A*02:01 23.4 0.12 0.87 0.78 Y 312.5 Trunk
2 MPEGTACV AS-derived (RI) DAB2 HLA-A*02:01 34.7 0.18 0.84 0.72 Y 198.3 Trunk
3 WQRTYKPL AS-derived (SE) MAGI2 HLA-A*24:02 56.1 0.25 0.79 0.65 Y 145.2 Trunk
4 GHNWAVTL AS-derived (A3SS) FHIT HLA-A*02:01 67.8 0.31 0.76 0.61 - 89.7 Subclonal
5 KPFVYVLA AS-derived (MXE) PKM HLA-B*07:02 89.2 0.38 0.72 0.55 - 567.4 Trunk
6 TNSLADTN AS-derived (SE) KIF1B HLA-A*02:01 112.3 0.44 0.69 0.51 - 78.9 Subclonal
7 QVLPAGVA AS-derived (A5SS) MACF1 HLA-A*24:02 134.5 0.52 0.66 0.48 - 123.4 Trunk
8 HRLPAGSI AS-derived (RI) USP47 HLA-A*02:01 156.7 0.61 0.63 0.44 - 56.2 Subclonal
9 DLFSGTNV AS-derived (SE) FAT1 HLA-B*44:03 178.9 0.68 0.6 0.41 - 34.5 Subclonal
10 VTEPVLKA AS-derived (MXE) CALD1 HLA-A*02:01 198.2 0.74 0.58 0.38 - 167.8 Trunk

7c: Fusion-Derived Neoepitopes

RankPeptideFusionHLAIC50 (nM)Rank %Imm. ScoreTCR ProbMSTPMClonality
1 GPPVYNTC DNAJB1-PRKACA HLA-A*02:01 41.3 0.19 0.81 0.69 Y 156.3 Trunk
2 KMEAFNRA TFEB-CLTC HLA-A*24:02 67.8 0.33 0.75 0.57 - 42.7 Subclonal
3 LPRGSPAA DNAJB1-PRKACA HLA-B*07:02 89.4 0.41 0.7 0.5 - 156.3 Trunk
Binding Affinity vs Immunogenicity (Top Candidates)

TCR Repertoire

12453
Total Clonotypes
7.8
Shannon Diversity
0.42
Clonality

Top Expanded Clonotypes

ClonotypeFrequencyExpansionSpecificity
TRBV9-TRBJ2-1_CASSDSNTGELFF 8.3% High Likely tumor-reactive
TRBV12-4-TRBJ2-7_CASSQAPRGTGELFF 5.6% Medium Unknown
TRBV20-1-TRBJ1-2_CASSLAPGATNEKLFF 4.1% Medium Likely tumor-reactive
TRBV6-4-TRBJ2-5_CASSDAGVSTDTQYF 3.2% Low Unknown
TRBV7-9-TRBJ2-3_CASSQETQYF 2.8% Low Unknown

TME Cell Composition

Immune Gene Signatures

SignatureScoreStatusInterpretation
Interferon-gamma -1.2 Low Reduced anti-tumor immune activation
T-cell inflamed -0.8 Low Cold TME — limited T-cell infiltration
Immune exclusion 1.5 High T cells excluded from tumor core by stromal barrier
WNT/β-catenin 1.8 High Associated with immune exclusion in HCC

Checkpoint Marker Expression

MarkerExpression (TPM)Status
PD-L1 (CD274) 45.3 Moderate
CTLA-4 12.7 Low
LAG-3 8.9 Low
TIM-3 (HAVCR2) 23.1 Moderate

Antagonistic Self-Peptide Analysis

Antagonistic self-peptides identified: 14

PeptideHLAAntagonism ScoreNote
VLPTDLSV HLA-A*02:01 0.78 Self-peptide with antagonistic TCR interaction — candidate for displacement
GMAKDSVAV HLA-A*24:02 0.71 Self-peptide suppressing TCR activation
KLPQAGSV HLA-B*07:02 0.65 Moderate antagonism — displacement candidate

Peptide Vaccine Candidates (Top 8)

RankPeptideSourceRationaleConfidence
1 SLADTNSL AS-derived (TTN) Highest immunogenicity + MS-validated + trunk clonality High
2 MPEGTACV AS-derived (DAB2) MS-validated + high binding affinity + trunk High
3 GPPVYNTC Fusion (DNAJB1-PRKACA) MS-validated + high expression + trunk High
4 WQRTYKPL AS-derived (MAGI2) MS-validated + high tumor-specificity High
5 KLDKVNSL Mutation (TP53) Driver mutation + high immunogenicity Medium
6 KPFVYVLA AS-derived (PKM) High expression + trunk clonality Medium
7 STLPGVIAA Mutation (CTNNB1) Driver mutation + trunk Medium
8 GHNWAVTL AS-derived (FHIT) Good binding + tumor-specific Medium

TCR-T Cell Therapy Targets

PeptideHLARationaleConfidence
SLADTNSL HLA-A*02:01 Top candidate for TCR engineering — high TCR recognition probability (0.78) High
MPEGTACV HLA-A*02:01 MS-validated + high TCR recognition probability (0.72) High
GPPVYNTC HLA-A*02:01 Fusion-derived + MS-validated + trunk High

Combination Strategy

Primary: Personalized peptide vaccine (top 15 AS-derived neoepitopes) + anti-PD-L1

Immune-excluded TME with high PD-L1 expression suggests checkpoint blockade may release stromal barrier. AS-derived neoepitopes provide antigenic targets beyond mutation burden.

Secondary: Add self-peptide displacement peptides to counter antagonistic self-immunopeptidome

Monitoring: TCR repertoire tracking + ctDNA monitoring for response assessment

Self-Peptide Displacement Designs

Target Self-PeptideDisplacing PeptideRationale
VLPTDLSV SLADTNSL (engineered variant) Higher MHC affinity displaces antagonistic self-peptide while maintaining TCR activation
GMAKDSVAV WQRTYKPL (engineered variant) Competitive displacement with enhanced immunogenicity

Methods & Software

StepToolVersionNotes
DNA sequencing Illumina NovaSeq 6000 WES 300X tumor / 150X normal Augmented exome capture across 20,000 genes
Somatic variant calling Mutect2 (GATK 4.4.0) 4.4.0.0 Tumor-normal mode, PoN filtering
CNV calling CNVkit 0.9.10 Tumor-normal paired analysis
HLA typing OptiType 1.3.2 4-digit resolution from WES
HLA-LOH LOHHLA 1.0 Detected LOH at HLA-B*07:02
Long-read RNA-seq PacBio Revio (Iso-Seq) SMRT Link 13.0 Full-length isoform sequencing
Short-read RNA-seq alignment STAR 2.7.11b 2-pass mode, GENCODE v44
Expression quantification Salmon 1.10.1 Transcript-level TPM
AS event detection rMATS + LongGF 4.1.2 / 1.3 Tumor vs normal paired, FDR < 0.05
Fusion detection STAR-Fusion + Arriba 1.12.0 / 2.3.0 Consensus calls, ≥5 read support
Immunopeptidomics MSFragger + FragPipe 19.0 / 21.0 1% FDR, customized database including AS/fusion peptides
MHC-I binding prediction NetMHCpan-4.1 + MHCflurry-2.0 4.1 / 2.0 8-11mers, all patient HLA alleles
Immunogenicity prediction DeepImmuno + PRIME 2.0 / 1.0 Deep learning-based
Structural modeling AlphaFold2 + ColabFold 2.4 / 1.5.5 Peptide-MHC complex modeling
scRNA-seq processing Cell Ranger + Scanpy 7.2 / 1.9.5 10x Chromium, 5,000 cells
TCR repertoire MiXCR 4.0.0 TRB chain, productive rearrangements

QC Metrics

MetricValueStatus
WES mean coverage (tumor) 312X Pass
WES mean coverage (normal) 158X Pass
RNA-seq mapped reads 87.3% Pass
Long-read N50 2,847 bp Pass
MS/MS peptide IDs (1% FDR) 8,421 Pass
scRNA-seq cell count 5,234 Pass
TCR productive rearrangements 12,453 Pass
Tumor purity (estimate) 0.72 Pass
Contamination check None detected Pass

Limitations

  • Mock/demo data — not from a real patient. Values are programmatically generated for demonstration.
  • Immunogenicity predictions are computational estimates requiring experimental validation.
  • TCR recognition probabilities are model-based and require autologous T-cell assay confirmation.
  • Self-peptide displacement designs are computational proposals requiring in vitro binding competition validation.
  • TME deconvolution is estimated from bulk RNA-seq and scRNA-seq reference; absolute fractions may vary.

Disclaimer

FOR RESEARCH USE ONLY — Not for use in diagnostic procedures. This report was generated by the PeptideXme computational pipeline for research purposes. All findings require experimental validation before any clinical application.