In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.

Despite major advancements in lung cancer treatment, long-term survival is still rare, and a deeper understanding of molecular phenotypes would allow the identification of specific cancer dependencies and immune evasion mechanisms. Here we performed in-depth mass spectrometry (MS)-based proteogenomic analysis of 141 tumors representing all major histologies of non-small cell lung cancer (NSCLC). We identified six distinct proteome subtypes with striking differences in immune cell composition and subtype-specific expression of immune checkpoints. Unexpectedly, high neoantigen burden was linked to global hypomethylation and complex neoantigens mapped to genomic regions, such as endogenous retroviral elements and introns, in immune-cold subtypes. Further, we linked immune evasion with LAG3 via STK11 mutation-dependent HNF1A activation and FGL1 expression. Finally, we develop a data-independent acquisition MS-based NSCLC subtype classification method, validate it in an independent cohort of 208 NSCLC cases and demonstrate its clinical utility by analyzing an additional cohort of 84 late-stage NSCLC biopsy samples.

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PNI and T stage and positive lymph nodes are independent markers of poor prognosis in patients with gastric cancer. PNI should be incorporated in the postoperative staging system for planning follow-up after surgery and in our opinion to propose more aggressive postoperative therapies in PNI-positive patients.

Our findings raise the possibility that downregulation of KAI-1/CD82 in TPC cells is one of the molecular mechanisms regulating their invasive and metastatic potential.

Pleomorphic adenoma is a common benign salivary gland tumor, which represents about 66 % of benign neoplasms of the salivary glands. Although it can occur in any salivary gland, it is most frequently found in the parotid. Pleomorphic adenomas are renowned for their cytomorphological and architectural heterogeneity that are characterized by intermixed epithelial and mesenchymal-like components. We report a rare case of pleomorphic adenoma of the parotid gland with prevalent schwannoma-like features mimicking a benign schwannoma. Microscopically the tumor showed a prevalence (about 95 %) of schwannoma-like areas with focal (about 5 %) epithelial component with tubular organization. The tumor showed positive immunoexpression for cytokeratin, S-100 protein, and focal expression of p63, CD10 and smooth muscle actin. To the best of our knowledge only six cases of schwannoma-like pleomorphic adenoma have been reported in the literature. The differential diagnosis between this entity and neurogenic and myogenic tumors is discussed.

Pure adenocarcinomas of the urothelium are very rare and their location in the pelvis is uncommon. Although their pathogenesis is not well defined, adenocarcinomas are likely to originate from neoplastic transformation of the glandular cells of the urothelial intestinal metaplasia usually arising in response to chronic irritating stimuli, such as long-duration inflammation, urolithiasis, and hydronephrosis. We report a case of an 81-year-old woman who underwent right nephrectomy for relapsing renal abscess due to a staghorn calculus. Histological examination disclosed an infiltrating adenocarcinoma arising from a tubulovillous adenoma with the surrounding pelvic mucosa showing a sequence of intestinal metaplasia, low- and high-grade villous adenoma, and invasive adenocarcinoma, supporting the hypothesis of cancer progression due to chronic inflammation from the urothelium through the metaplasia step.

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