Clonal expansion of T-cells is a feature that has been observed in solid cancers after ICB.(13) In line with this interpretation, bulk analysis of localized treatment naive breast cancer (BC) specimens showed a higher clonality (median SC = 0.0429) compared to reactive lymph nodes (RLN; median SC = 0.0072) which served as a control (p = 0.0007, Fig. 1A). In contrast, the TME of treatment naive HL displayed a rather polyclonal TCR pattern. Clonality in HL biopsies (median SC = 0.0115) was only slightly higher than in reactive lymphoid tissue and significantly lower compared to BC (Fig. 1A, p = 0.014 and p = 0.0003, respectively). The content of unique single copy TCR sequences (singletons) showed a distribution inverse to clonality. Polyclonal specimen, such as RLN and HL, displayed the highest percentage of singletons (Supplementary Fig. 1A) Thus, T-cells in the TME of treatment naive HL are highly diverse and clonal expansion seems minimal by bulk TCR analysis. Clonally expanded T-cells, i.e. presumably lymphoma-specific T-cells, are thus either absent or present only as small populations which might be locally prevented from expansion in the TME of HL. To distinguish these two possibilities, we first searched for TCR sequences of known specificity against Epstein-Barr-Virus (EBV) and correlated their presence with the detection of EBV in HRSC detected by LMP1 immunohistochemistry or EBER in situ hybridization.(8) We did not detect an enrichment of TCR sequences annotated to be EBV-specific in HL with EBV-positive versus EBV-negative HRSC in two independent cohorts of treatment naive HL comparing 12 EBV + versus 73 EBV- cases and 11 EBV + versus 43 EBV- cases, respectively (Supplementary Fig. 2 + 3). Unfortunately, public databases are limited in the number of TCR sequences annotated for EBV proteins which are expected in HRSC (EBNA1, LMP1, LMP2a) and the number or TCR sequences obtained in our analysis varies (Supplementary Table 3). Thus, our analysis suffers from low sensitivity. Nevertheless, we consider the absence or at least low frequency of EBV-specific TCR sequences in EBV-positive HL in combination with the polyclonality of TCR repertoires to support the hypothesis of a TME mostly devoid of specific T-cells directed against the neoplastic cells in HL.
Next, we analyzed TCR dynamics between multiple biopsies of the same patients to identify expansion of TCR as a surrogate for an anti-lymphoma immune reaction of T-cells. First, we analyzed bulk TCR clonality in pairs of primary and relapse samples of the same patient. We consider these episodes of clinical re-occurrence as a model of re-exposure of the immune system to the same tumor. Two consecutive biopsies of RLN (RLN and RLN 2nd ) in the same patient served as control. We did not detect an increase of clonality in BC specimens between primary and relapse biopsies probably because maximum levels of clonality have already been reached at first presentation (Fig. 1B). However, HL specimens displayed higher TCR clonality at relapse after conventional chemotherapy (Fig. 1B, p < 0.0001). Again, the percentage of singletons was inversely proportional to clonality (Supplementary Fig. 1B). The finding in HL suggests that HL prevents clonal expansion in the treatment naïve TME but clonal expansion is gradable at relapse. Of note, even at relapse, TCR clonality in HL was lower compared to treatment naive BC specimen (p = 0.047, Fig. 1B, Supplementary Table 4) indicating that even at re-occurrence an accumulation of clonally expanded T-cells is hampered in the HL TME.
To better understand TCR dynamics, we analyzed subsets of TCR sequences defined by their frequency in the first biopsy. To this end, TCR sequences detected in the primary biopsy were separated into single-copy (singletons) and multiple-copy TCR sequences (non-singletons), the latter reflecting pre-amplified clones(9). The expansion of singletons and non-singletons was studied comparing the primary and relapse biopsy as defined in the Methods Section. Expansion of singletons and non-singletons in RLN (comparing a first and the subsequent biopsy of the same patient) was assessed to define random TCR dynamics in lymphoid tissue at multiple timepoints (Fig. 1C and 1D). As expected, based on the definition of singletons, the level of expansion is higher in singletons than in non-singletons. In paired biopsies of HL, expanded singletons and non-singletons were not significantly different than in reactive lymphoid tissue. In contrast, BC specimens displayed an expansion of non-singletons at relapse that was higher than in reactive tissue and HL (Fig. 1C and 1D, p = 0.001 and p = 0.004, respectively). These data show that in BC pre-amplified TCR clones (non-singletons) expand at relapse in the TME - a finding compatible with the scenario of a re-exposure of a primed immune system to the antigenic repertoire of this solid cancer. In contrast, clonal expansion of pre-amplified T-cell clones appears to be effectively prevented in primary, treatment-naive HL as well as at relapse. This phenomenon may be explained by (i) ineffective immune priming in treatment-naive HL (anergy) (ii) blockade of clonal expansion of lymphoma-specific T-cells despite their presence in the TME (inhibition) or (iii) prevention of infiltration by primed, clonally pre-expanded T-cells (exclusion) at relapse. Of note, our analysis evaluates bulk tumor/TME. We have no access to single-cell data which may allow detection of small T-cell clones that escape bulk TCR analysis.(14) Nevertheless, our findings suggest that the increase in clonality of relapsed HL is not linked to expansion of preexisting clones. To further evaluate this hypothesis, we analyzed the TCR clone overlap in the treatment-naïve TME with the TME at relapse. Reactive lymph nodes with first and sequential biopsy from the same patient served as a negative control. The percentage of clones in the treatment-naïve TME that were also detected at relapse was significantly higher in BC than in HL and RLN (Fig. 1E, p = 0.0002 and p = 0.001, respectively), whereas we observed no significant differences between HL and RLN. These findings are in line with low level of clonal expansion in the TME of HL compared to BC and support the hpothesis that the observed increased clonality in HL at relapse (Fig. 1B) is not linked to expansion of preexisting clones.
To gain further insight into the pathomechanism inhibiting clonal expansion of T-cells in the TME of HL and to distinguish anergy, inhibition and exclusion, we analyzed bulk TCR sequences in sequential biopsies of HL and hepatocellular carcinoma (HCC) obtained during ICB, which is expected to unleash previously inhibited clonal expansion of T-cells. Sequential RLN biopsies served as a control of random expansion of TCR sequences over time. Neither in HCC nor HL an increase of clonality was detected when treatment naive biopsies were compared to specimens obtained during ICB (Fig. 2A). It is important to mention that re-biopsies of HL patients were obtained during the period of time when ICB exerts its clinical effects, i.e. in patients responding to anti-PD1-based first-line treatment.(8) Since clonality is already high in HCC prior to ICB (median SC = 0.0606), a maximum level of clonality may have already been reached in this solid cancer. In HL, however, clonality was significantly lower (median SC = 0.0115) than in HCC, but not further increased by ICB as reported previously2 (Fig. 2A, p = < 0.0001 prior and p = 0.001 under ICB). Next, we tested for expansion of singletons and non-singletons in sequential biopsies of HCC and HL during ICB to identify TCR repertoire dynamics. In HL and HCC, singletons did not expand at a significantly higher level compared to RLN when two sequential biopsies of the same patient were compared (Fig. 2B). In contrast, clonal expansion of non-singletons during ICB differed between HCC and HL. In comparison to control tissue, pre-expanded non-singletons were significantly more frequently expanded in HCC following ICB (Fig. 2C, p = 0.029), whereas no significant difference to RLN was observed in HL under ICB (Fig. 2C). Next, we analyzed the clone overlap in the treatment-naïve TME with the TME under ICB. As already observed for relapsed BC, the percentage of clones in the treatment-naïve TME that were also detected during ICB was significantly higher in HCC than in HL and RLN (Fig. 2D, p = 0.018 and p = 0.0006, respectively). Again, we observed no significant differences between HL and RLN. We hence conclude that, both conditions - re-exposure to the cancer at relapse or immune activation by ICB – are associated with re-occurrence of preexisting TCR clones and expansion of predominantly pre-amplified T-cell populations in the TME of solid cancers, but this phenomenon is not detectable in HL.
To evaluate the contribution of exclusion of lymphoma-specific T-cells from the TME to the observed TCR polyclonality in the HL TME, we analyzed peripheral blood mononuclear cells (PMBC) of HL patients during ICB-based first-line treatment. First, we analyzed bulk PBMC containing all types of T-cells. As expected, healthy controls showed the lowest clonality (Fig. 3A, median SC = 0.0109). Bulk analysis of TCR repertoires in PBMC is obviously able to identify TCR expansion in immune reactions since CMV infected patients showed significantly higher clonality (median SC = 0.0342) than healthy controls (Fig. 3A, p = < 0.0001). Interestingly, PBMC of treatment-naïve HL patients showed higher clonality (median SC = 0.0369) than healthy controls indicating clonal TCR expansions in the peripheral blood of HL patients before any therapy and in contrast to the findings in TME (p < 0.0001, Fig. 3A, percentage of singletons see Supplementary Fig. 4A). However, increased TCR clonality in the blood is not specific for HL patients since the PBMC of patients suffering from HCC displayed similarly high clonality (Fig. 3B, median SC = 0.0507) as reported previously.(15) Although the PBMC of treatment-naïve HL and those obtained at relapse are not derived from the same patients and therefore, it is not possible to determine non-singleton expansion, it still appears notable that clonality is higher at relapse (Fig. 3B, median SC = 0.0701, p = 0.0004, percentage of singletons see Supplementary Fig. 4B). In line with the findings in tissue biopsies, TCR clonality in PBMC did neither increase in treatment-naïve HL nor in relapsed HL during and after ICB (Fig. 3C, percentage of singletons see Supplementary Fig. 4C). Similar results were obtained when the time points during and after ICB were analyzed separately (Supplementary Table 5). Clonal expansion during and after ICB did not differ between treatment-naïve HL and relapsed HL (Fig. 3D and Supplementary Fig. 4D).
The increase in clonality and decrease in percentage of singletons in the peripheral blood of HL patients at relapse may present increased expansion of T-cell populations upon re-exposure of the immune system to the lymphoma. The discrepancy in clonality between TME and blood suggests that T-cell expansions in HL patients may occur more effectively outside the TME at other sites of the body. However, in contrast to solid cancers, the clonally expanded T-cells do not seem to enter the TME efficiently, resulting in the observed discrepantly lower TCR clonality in the HL TME than the peripheral blood. To find more evidence for exclusion of clonally expanded peripheral blood T-cells from the TME, we analyzed the overlap of clones between tissue and peripheral blood. The percentage of TCR sequences in the TME that were also detected in the peripheral blood of the same patient was significantly higher in HCC compared to HL specimens (Fig. 4A, p < 0.0001 prior and p = 0.003 under ICB). Of note, the percentage of clone overlap did not increase during ICB for both entities (Fig. 4A).
To understand if T-cell subtypes may exhibit clonal expansion that is missed in bulk PBMC analyses, we used sorted CD4 + and CD8 + PBMC obtained before, during and after ICB as first-line therapy for HL. We observed increased clonality of CD8 + compared to CD4 + PBMC of HL patients at all time-points (Fig. 4B, p = 0.016 before ICB, p = 0.0006 during ICB, p = 0.004 after ICB). However, clonality did not change in any T-cell type during ICB (Fig. 4B and Supplementary Table 5, percentage of singletons: Supplementary Fig. 5A). Thus, ICB does not induce obvious clonal expansion of CD4 + or CD8 + T -cells in peripheral blood during anti-PD1-based first-line treatment of HL patients. Re-analysis of an independent cohort of refractory/relapsed HL yielded similar results (Supplementary Fig. 6 and Supplementary Table 5). Analyzing the dynamic changes during ICB, we found that singletons did not expand differently in CD4 + and CD8 + cells (Supplementary Fig. 5B). In contrast, non-singletons expanded significantly higher in CD8 + compared to CD4 + cells (p = 0.0095, Fig. 4C). Thus, under ICB, clonal expansion in the blood of HL patients predominantly affects CD8 + cells and mostly pre-amplified T-cell populations (non-singletons).