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Tumour-specific CD8 T cell dysfunction is a differentiation state that is distinct from the functional effector or memory T cell states 1 – 6 . Here we identify the nuclear factor TOX as a crucial regulator of the differentiation of tumour-specific T (TST) cells. We show that TOX is highly expressed in dysfunctional TST cells from tumours and in exhausted T cells during chronic viral infection. Expression of TOX is driven by chronic T cell receptor stimulation and NFAT activation. Ectopic expression of TOX in effector T cells in vitro induced a transcriptional program associated with T cell exhaustion. Conversely, deletion of Tox in TST cells in tumours abrogated the exhaustion program: Tox -deleted TST cells did not upregulate genes for inhibitory receptors (such as Pdcd1 , Entpd1 , Havcr2 , Cd244 and Tigit ), the chromatin of which remained largely inaccessible, and retained high expression of transcription factors such as TCF-1. Despite their normal, ‘non-exhausted’ immunophenotype, Tox -deleted TST cells remained dysfunctional, which suggests that the regulation of expression of inhibitory receptors is uncoupled from the loss of effector function. Notably, although Tox -deleted CD8 T cells differentiated normally to effector and memory states in response to acute infection, Tox -deleted TST cells failed to persist in tumours. We hypothesize that the TOX-induced exhaustion program serves to prevent the overstimulation of T cells and activation-induced cell death in settings of chronic antigen stimulation such as cancer. The nuclear factor TOX is highly expressed in antigen-specific dysfunctional T cells in tumours and exhausted T cells during chronic viral infection and is a crucial regulator of the differentiation of tumour-specific T cells.

Chromosomal instability (CIN) is a driver of cancer metastasis 1 – 4 , yet the extent to which this effect depends on the immune system remains unknown. Using ContactTracing—a newly developed, validated and benchmarked tool to infer the nature and conditional dependence of cell–cell interactions from single-cell transcriptomic data—we show that CIN-induced chronic activation of the cGAS–STING pathway promotes downstream signal re-wiring in cancer cells, leading to a pro-metastatic tumour microenvironment. This re-wiring is manifested by type I interferon tachyphylaxis selectively downstream of STING and a corresponding increase in cancer cell-derived endoplasmic reticulum (ER) stress response. Reversal of CIN, depletion of cancer cell STING or inhibition of ER stress response signalling abrogates CIN-dependent effects on the tumour microenvironment and suppresses metastasis in immune competent, but not severely immune compromised, settings. Treatment with STING inhibitors reduces CIN-driven metastasis in melanoma, breast and colorectal cancers in a manner dependent on tumour cell-intrinsic STING. Finally, we show that CIN and pervasive cGAS activation in micronuclei are associated with ER stress signalling, immune suppression and metastasis in human triple-negative breast cancer, highlighting a viable strategy to identify and therapeutically intervene in tumours spurred by CIN-induced inflammation. Chromosomal instability in cancer is linked to endoplasmic reticulum stress signalling, immune suppression and metastasis, which is mediated by the cGAS–STING pathway, suppression of which can reduce metastasis.

Rare subtypes of triple-negative breast cancers (TNBC) are a heterogenous group of tumors, comprising 5–10% of all TNBCs. Despite accounting for an absolute number of cases in aggregate approaching that of other less common, but well studied solid tumors, rare subtypes of triple-negative disease remain understudied. Low prevalence, diagnostic challenges and overlapping diagnoses have hindered consistent categorization of these breast cancers. Here we review epidemiology, histology and clinical and molecular characteristics of metaplastic, triple-negative lobular, apocrine, adenoid cystic, secretory and high-grade neuroendocrine TNBCs. Medullary pattern invasive ductal carcinoma no special type, which until recently was a considered a distinct subtype, is also discussed. With this background, we review how applying biological principals often applied to study TNBC no special type could improve our understanding of rare TNBCs. These could include the utilization of targeted molecular approaches or disease agnostic tools such as tumor mutational burden or germline mutation-directed treatments. Burgeoning data also suggest that pathologic response to neoadjuvant therapy and circulating tumor DNA have value in understanding rare subtypes of TNBC. Finally, we discuss a framework for advancing disease-specific knowledge in this space. While the conduct of randomized trials in rare TNBC subtypes has been challenging, re-envisioning trial design and technologic tools may offer new opportunities. These include embedding rare TNBC subtypes in umbrella studies of rare tumors, retrospective review of contemporary trials, prospective identification of patients with rare TNBC subtypes entering on clinical trials and querying big data for outcomes of patients with rare breast tumors.

Introduction Breast cancer, especially triple-negative breast cancer (TNBC), lacks sensitive and specific diagnostic markers that can reliably differentiate it from carcinomas of other origins. TRPS1 is a relatively new immunohistochemical (IHC) marker that has demonstrated higher sensitivity in breast cancer, including TNBC. However, with the increasing use of this marker, broader immunoreactivity has been observed. This study aims to evaluate the utility of TRPS1 for establishing carcinoma of mammary origin. We compared the diagnostic sensitivity and specificity of TRPS1 with that of other IHC markers (GATA3 and SOX10). Methods In this retrospective study, we reviewed TRPS1 IHC performed at our center between 07/2022 and 06/2024, to evaluate the expression of TRPS1 in breast carcinoma (primary and distant metastasis) and in other malignancies. The sensitivity and specificity of TRPS1 in determining carcinoma of breast origin were compared with those of GATA3 and SOX10. Results The study cohort comprised 106 cases, including 17 cases at the primary site, and 89 samples of distant metastasis. After correlation with morphology, immunophenotype and molecular studies, 94 cases (88.7%) were characterized as breast primary (37.9% ER+/HER2neu-, 4.6% ER-/HER2neu+, 1.1% ER+/HER2neu+, 56.3% TNBC), whereas 12 (11.3%) were non-breast primary. The non-breast primary sites included lung, bladder, Mullerian, and gastrointestinal. The sensitivity and specificity of TRPS1 were 93.6% and 58.3%, respectively. Conversely, GATA3 demonstrated a sensitivity and specificity of 76.9% and 66.7%, respectively. SOX10 exhibited the lowest sensitivity at 47.9%, but with the highest specificity at 100%. There were three cases of metastatic breast carcinoma (sites: bladder, lung, and bone), where TRPS1 was the only positive marker, whereas GATA3 and SOX10 were negative. TRPS1 showed a higher positivity rate (92.0%) in TNBC compared to GATA3 (63.4%) and SOX10 (56.7%). TRPS1 expression was also observed in other tumor types, including carcinoma of Mullerian origin, bladder, and lung, limiting its utility in the differential diagnosis. Conclusion Our study demonstrated a higher sensitivity of TRPS1 expression in establishing carcinoma of breast origin compared with GATA3 and SOX10, consistent with previous reported studies. However, the specificity of TRPS1 was lower than that of GATA3 and SOX10. These findings suggest that while TRPS1 can be used as a reliable marker for breast cancer, its expression in other tumor types should be carefully interpreted to avoid diagnostic pitfalls.

Background/ObjectiveCancers classified as “special histologic subtypes” are felt to have a good prognosis. We used the 21-gene Oncotype DX Breast Recurrence Score® multigene assay to examine prognostic variation within special histologic subtypes. We also examined the Recurrence Score® (RS) distribution among the more common ductal (IDC) and lobular (ILC) cancers.Methods610,350 tumor specimens examined in the Genomic Health clinical laboratory from 2/2004 to 8/2017 were included. Specimen histology was classified centrally using a single H&E slide and World Health Organization criteria. RS distribution (low < 18, intermediate 18–30, and high ≥ 31) was compared among histologic subtypes.ResultsMedian patient age was 60 years (IQR 51–67); 80% were node negative. Most patients had low RS results (59.2%); only 9.5% had high results. The lowest mean RS was seen in the papillary subtype (11); the highest in the IDC group (18.4). Mean RS for all special subtypes was lower than that of IDC patients. When the high RS threshold was decreased from 31 to 25, as used in the TAILORx and RxPONDER trials, the number of high RS-result patients increased from 9.5% to 16.8%. Patients with ILC had a lower mean RS result than patients with IDC, 16.5 versus 18.4.ConclusionThere is substantial diversity in predicted prognosis among patients with cancers classified as special histologic subtypes, with 12–25% having intermediate RS results and 0.5–9% having high RS results. Pending further definition of the role of chemotherapy for patients with intermediate RS results by TAILORx and RxPONDER, the RS result may help to inform systemic therapy decisions in these patients.

Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA , among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively ‘featureless’ surface dominated by the peptide’s backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA -mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA -derived public NeoAg. A new high-throughput platform to find rare T cells that can recognize shared cancer neoantigens identifies T cell receptors specific for a conserved, immunogenic and therapeutically actionable epitope in mutant PI3Kα, one of the most common driver oncogenes

PurposeHuman epidermal growth factor receptor 2 (HER2)-positive breast cancers are known to have significant clinical and pathological response to neoadjuvant systemic therapy (NST). The aim of this study was to identify factors associated with pathological complete response (pCR), defined as no residual invasive carcinoma in the breast and axillary lymph nodes (ypT0/is ypN0), among patients with HER2-positive breast cancer and to compare pCR rates between breast cancers with HER2 protein overexpression by immunohistochemistry (IHC) versus HER2 gene amplification by fluorescence in situ hybridization (FISH) in the absence of protein overexpression by IHC.MethodsWe conducted a retrospective review of HER2-positive breast cancer patients treated with NST and surgery at Memorial Sloan Kettering Cancer Center between January 2013 and May 2018. Estrogen receptor (ER), progesterone receptor (PR), and HER2 status were assessed according to the 2018 ASCO/CAP guidelines.ResultsDuring the study period, 560 patients were identified. Of 531 patients with IHC results available, 455 patients had HER2 IHC 3+, and 76 had IHC < 3+ but HER2 amplification detected by FISH. The overall pCR rate was 59% (330/560). The pCR rate among patients with HER2 protein overexpression (IHC 3+) was 67%, compared to 17% among patients with HER2 amplification by FISH (IHC < 3+). On univariate and multivariate analyses, HER2 protein overexpression by IHC (IHC 3+) was a significant predictor of pCR, along with grade 3 histology, PR-negative status, and dual anti-HER2 therapy.ConclusionAlthough both HER2 IHC and FISH are standard HER2 testing methods in breast cancer, achievement of pCR is associated with HER2 IHC expression level, among other factors.

Metaplastic breast carcinoma (MpBC) is a rare special histologic subtype of breast carcinoma characterized by the presence of squamous and/or mesenchymal differentiation. Most MpBCs are of triple-negative phenotype and neoadjuvant chemotherapy (NAC) is frequently utilized in patients with MpBC. The aim of this study was to evaluate response to NAC in a retrospective cohort of MpBCs. We identified 44 patients with MpBC treated with NAC at our center between 2002 and 2018. Median age was 48 years, 86% were clinical stage II–III, and 36% were clinically node-positive. Most (80%) MpBCs were triple-negative or low (1–10%) hormonal receptor positive and HER2 negative on pre-NAC biopsy. While on NAC, 49% showed no clinical response or clinico-radiological progression. Matrix-producing subtype was associated with clinico-radiological response (p = 0.0036). Post NAC, two patients initially ineligible for breast-conserving surgery (BCS) were downstaged to be eligible for BCS, whereas three patients potentially eligible for BCS before treatment became ineligible due to disease progression. Only one (2%) patient had a pathologic complete response (pCR). Among the 16 patients presenting with biopsy-proven clinical node-positive disease, 3 (19%) had nodal pCR. Axillary lymph node dissection was avoided in 3 (19%) patients who had successful axillary downstaging. Residual cancer burden (RCB) was assessed in 22 patients and was significantly associated with disease-free survival and overall survival. We observed a poor response or even disease progression on NAC among patients with MpBC, suggesting that NAC should be reserved for patients with inoperable MpBC.

Background The benefit of neoadjuvant chemotherapy (NAC) in patients with estrogen receptor-positive (ER+)/human epidermal growth factor receptor 2-negative (HER2−) breast cancers and in invasive lobular carcinoma (ILC) is uncertain due to the low rates of pathologic complete response (pCR). Objective The aim of this study was to determine if pathologic features can identify subsets likely to benefit from NAC. Methods Patients with stage I–III ER+, HER2− breast cancer receiving NAC were retrospectively reviewed. Endpoints were downstaging to breast-conserving surgery (BCS) and nodal pCR after NAC. Patients were grouped by progesterone receptor (PR) status and grade/differentiation (high grade or poor [HP] vs. non-HP). Results From 2007 to 2016, 402 ER+/HER2− cancers in patients receiving NAC were identified. Median age was 50 years, 98% were clinical stage II–III, and 75% were cN+. Overall pCR rate was 5%; breast pCR in 7% and nodal pCR in 15% of cN+ patients ( p  < 0.0001). Patients with ILC initially ineligible for BCS ( n  = 56) were less likely to downstage than those with invasive ductal carcinoma (IDC; n  = 183, 16 vs. 48%, p  ≤ 0.0001), with a similar trend in the axilla ( p  = 0.086). The rates of BCS eligibility after NAC were highest in PR−/HP patients (62%) and lowest in PR+/non-HP patients (29%) [ p  = 0.005]. In the axilla, nodal pCR among cN+ patients ( n  = 301) ranged from 0 to 35% ( p  < 0.0001) within these groups, and was most frequent in PR−/HP patients. Conclusions ER+/HER2− patients most likely to benefit from NAC are those with PR− and HP tumors. Patients with ILC are unlikely to downstage in the breast or axilla compared with IDC. The use of these criteria can assist in defining the initial treatment approach.

Immunohistochemistry techniques have been incorporated into surgical pathology for nearly a half-century and have since become intimately intertwined with its practice. In the realm of breast pathology, immunohistochemistry serves several purposes, including providing crucial prognostic and predictive data. Among its other applications, assessment of stromal invasion and establishment of mammary origin are crucial from a diagnostic standpoint. In these regards, sole reliance on immunohistochemistry may lead to misdiagnosis. In this review, we highlight pitfalls of immunohistochemistry commonly encountered in the practice of breast pathology and emphasize the importance of careful histopathological evaluation.