🛡️ Immune repertoire (TCR/BCR)

TRUST4 assembles T-cell and B-cell receptor sequences — including the hypervariable CDR3 — directly from the RNA-seq reads, reconstructing the immune cells that were present in each sample. It was run on the same three RNA BAMs as the rest of this site (the hand primary, the lung metastasis, and a normal-lung baseline), and independently reproduces the picture from oncoanalyser's CIDER: the hand primary is nearly devoid of B cells while both lung samples carry large, class-switched, B-cell–dominated repertoires.

The question this page explores: among the antibody (IG) clones in the lung metastasis, are any enriched there relative to normal lung — a possible, though unproven, signature of a local response to the tumor? The short answer is that the two lung repertoires overlap only slightly (Jaccard 0.045), but most of that is shallow sampling of a very diverse repertoire, not biology. The useful output is therefore not the raw "met-only" list but a ranked shortlist of expanded, class-switched, met-enriched clones — leads to follow up, not conclusions.

How to read this: start with the composition and isotype charts to see the B-cell–heavy, IgA-dominant lung repertoires. The clonality tiles show the metastasis is not more clonally expanded or mutated than normal lung — the key caveat. Then the overlap section ranks candidate met-enriched clones (sort the table by any column); the expression panel shows whether the tissue's B-cell microenvironment supports a local response at all. Everything here is hypothesis-generating: sequence cannot prove that a clone recognizes the tumor — that needs antibody-reconstruction binding assays.

Repertoire composition by locus

Productive CDR3 clonotypes assembled per locus. The hand primary is nearly devoid of B-cell (IG) clones and carries only a few T-cell (TR) clonotypes; both lung samples carry large, B-cell–dominated repertoires (IGK > IGL ≈ IGH ≫ T cells). Counts are normalized to library size (per million Isofox fragments) so samples of different depth compare fairly.

Left hand (primary)Lung metastasisNormal lung (baseline)

IGH

0.00

9.03

13.1

IGK

0.00

22.9

20.3

IGL

0.05

15.3

12.0

TRA/TRD

0.19

0.90

1.35

TRB

0.22

1.12

2.26

TRG

0.02

0.09

0.15

Antibody class (isotype) mix

Heavy-chain isotype of each B-cell clone. Both lung repertoires are dominated by IgA (the mucosal default in lung) with a class-switched IgG component and little naive IgM — an antigen-experienced, class-switched profile.

IgM· naive / unswitchedIgG· class-switchedIgA· mucosal (switched)ND· isotype not resolved

Hand (primary) (0 IGH)

no IGH clones detected

Lung met (1,092 IGH)

IgG 8%

IgA 59%

ND 30%

Normal lung (1,411 IGH)

IgG 9%

IgA 52%

ND 33%

Clonal expansion & maturation (IGH)

A tumor-driven B-cell response would show as more clonal expansion or more somatic hypermutation at the metastasis. Here the two lung repertoires are similar — the metastasis is not more oligoclonal or more mutated than normal lung — an important caveat for interpreting the clone overlap below.

Left hand (primary)

0IGH clones

—clonality

—top clone

—CDR3 germline sim

Lung metastasis

1,092IGH clones

0.102clonality

3.6%top clone

95.5%CDR3 germline sim

Normal lung (baseline)

1,411IGH clones

0.138clonality

3.1%top clone

95.8%CDR3 germline sim

Lung metastasis vs normal lung — heavy-chain overlap

IGH clones (by CDR3 amino acid) shared between the two same-batch lung samples vs private to each. Overlap is low (Jaccard 0.045) — expected when a diverse repertoire is sampled shallowly, so most "met-only" clones are sampling, not biology. The interesting subset is the ranked candidates below: expanded, class-switched, met-enriched clones.

985

1,304

Lung metastasis only · 985Shared (both) · 107Normal lung (baseline) only · 1,304

Candidate met-enriched clones

Ranked by a transparent composite of expansion × class-switch × met-enrichment (shown as Score). These are hypothesis-generating leads, not validated tumor-reactive antibodies — sequence alone cannot prove specificity.

What each column means

CDR3 (aa): The CDR3 amino-acid sequence — the hypervariable loop that forms the core of the antigen-binding site and defines the clone. Two clones with the same CDR3 aa are treated as one here.
V: The germline V·J gene segments this clone recombined (V shown, J after the dot) — its genetic family, e.g. IGHV3-33·IGHJ6.
Isotype: Antibody class, from the constant (C) gene: IgM (naive / unswitched) vs class-switched IgG or IgA. IgG (red) is the affinity-matured, antigen-experienced class most associated with a directed response.
Met reads: RNA-seq reads supporting this clone in the lung metastasis — a proxy for how expanded (abundant) the clone is.
Normal: Reads for the same CDR3 in the normal-lung sample. 0 (green) means the clone was not detected in normal lung — i.e. met-only.
SHM %sim: Somatic-hypermutation proxy: percent similarity of the CDR3 to its germline. Lower = more mutated = more affinity-matured (~100% ≈ near-germline).
Signals: Flags that raise interest: met-only (absent from normal lung), IgG (class-switched), and convergent (the same CDR3 aa assembled from ≥2 independent nucleotide rearrangements — a signature of antigen-driven selection).
Score: A transparent prioritization only: expansion (met reads) × class-switch weight × met-enrichment. Higher = stronger candidate. Not a probability or a measure of tumor-reactivity.

CDR3 (aa)ⓘ	Vⓘ	Isotypeⓘ	Met readsⓘ	Normalⓘ	SHM %simⓘ	Signalsⓘ	Scoreⓘ ▾
CARDSSGYGRGFGGRYYYGMDVW	IGHV3-33·IGHJ6	IGHA1	213	0	95.6	met-only	554
CARGTGSHRSGWPYFDYW	IGHV3-21·IGHJ4	IGHA1	140	0	97.1	met-only	364
CARERRRDVWGSYRYRKAFDIW	IGHV3-23·IGHJ3	IGHA1	87	22	93.8	convergent	339
CARISPGGHGFDVW	IGHV1-18·IGHJ3	IGHG3	71	0	93.1	met-only IgG convergent	256
CAKVLSLTENYWYGMDVW	IGHV3-23·IGHJ6	IGHA1	49	13	94.7		191
CTRDWGVVVLPAAMGFDYW	IGHV3-49·IGHJ4	IGHA1	49	6	97.8	convergent	191
CAKDWGGLLMNNWYFDLW	IGHV3-23·IGHJ2	IGHA1	45	12	97.5		176
CARGDWFDPW	IGHV1-3·IGHJ5	IGHA1	44	4	97.1	convergent	172
CVREGYGDYGDYW	IGHV3-21·IGHJ4	IGHA1	42	9	94.1	convergent	164
CARQKIAAAGRRYYYYGMDVW	IGHV4-59·IGHJ6	IGHA1	57	0	100.0	met-only	148
CARKRRGDRYPFDFW	IGHV1-3·IGHJ4	IGHG2	32	0	93.3	met-only IgG	115
CARNAYFYGWYLDLW	IGHV3-48·IGHJ2	IGHG3	21	6	90.0	IgG	113
CARDRVHGMDVW	IGHV1-18·IGHJ6	IGHM	35	2	94.7		105
CARDRYYDFWSGYFDYW	IGHV3-11·IGHJ4	IGHA1	38	0	100.0	met-only	99
CASGPMTTVTTDWYFDLW	IGHV5-51·IGHJ2	IGHA1	25	4	97.4		98
CTTPSPSYQLRRDYW	IGHV3-15·IGHJ4	IGHA1	35	0	96.2	met-only	91
CARLSVPTAFGVISHYDFW	IGHV1-2·IGHJ4	IGHG3	25	0	100.0	met-only IgG	90
CARDLGRWLQDAFDIW	IGHV1-2·IGHJ3	IGHA1	24	9	100.0		74
CAKDRAWVRSPRGDYFDYW	IGHV3-23·IGHJ4	IGHA1	19	3	93.8	convergent	74
CARDIFPHSSSFLYYFDYW	IGHV3-21·IGHJ4	IGHA1	28	0	94.7	met-only	73
CARGIYGDFPYFDYW	IGHV4-38-2·IGHJ4	IGHA1	27	0	97.1	met-only	70
CARRAYCDGDCTLFNYLYFGLDVW	IGHV5-51·IGHJ6	IGHG1	19	0	91.7	met-only IgG	68
CTKDVEPGGATRW	IGHV3-9·IGHJ4	IGHA2	26	0	88.9	met-only	68
CVRDWQWLEGRDCFDPW	IGHV1-18·IGHJ5	IGHA1	17	2	94.6		66
CARDLGKMAGASLDSW	IGHV3-48·IGHJ4	IGHG1	17	0	92.3	met-only IgG	61
CAKSDPNGVAAVFDYW	IGHV3-9·IGHJ4	IGHG1	16	0	100.0	met-only IgG	58
CASEAGYYYDSSGYYGDYW	IGHV3-21·IGHJ4	IGHA2	22	0	95.2	met-only	57
CAHRRETGDLFPPSPGFDYW	IGHV2-5·IGHJ4	IGHA1	22	0	100.0	met-only	57
CARIGLQHPYYYGMDVW	IGHV4-39·IGHJ6	IGHA1	17	6	97.5		56
CARDNDGPVVDGYNGIGYW	IGHV3-11·IGHJ4	IGHA1	20	0	94.1	met-only	52

B-cell microenvironment (expression context)

Isofox gene expression (AdjTPM, log scale) for B-cell, plasma-cell and tertiary-lymphoid-structure (TLS) markers. This says whether the tissue even supports a local B-cell response. The metastasis is plasma-cell / IgA-secretion skewed (high JCHAIN) but has fewer T cells and a weaker TLS signature than normal lung.

Hand (primary)Lung metNormal lung

B cell (CD20)

MS4A1

0.35

4.78

5.93

B cell (BCR)

CD79A

1.26

2.55

13.15

CD79B

1.62

3.65

10.18

B cell

CD19

0.11

0.43

2.42

Plasma cell

MZB1

0.11

7.58

11.54

XBP1

80.02

276.6

255.1

Plasma cell (Ig secretion)

JCHAIN

1.93

1006

353.4

Plasma cell (BLIMP1)

PRDM1

20.97

7.75

7.08

TLS (B-cell homing)

CXCL13

1.22

4.87

TLS (T-zone chemokine)

CCL19

36.16

74.23

135.4

CCL21

9.31

344.2

384.8

TLS (follicular DC, CD21)

CR2

0.07

0.57

0.48

TLS (lymphoid organogenesis)

LTB

1.32

7.05

25.95

T cell (context)

CD3D

0.56

29.14

56.74

CD8A

0.42

5.53

13.19

Bars are log₁₀(TPM+1)-scaled; values are AdjTPM.