| 1. |
- Briem, Oscar, et al.
(författare)
-
CD169+ Macrophages in Primary Breast Tumors Associate with Tertiary Lymphoid Structures, Tregs and a Worse Prognosis for Patients with Advanced Breast Cancer
- 2023
-
Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 15:4
-
Tidskriftsartikel (refereegranskat)abstract
- The presence of CD169+ macrophages in the draining lymph nodes of cancer patients is, for unknown reasons, associated with a beneficial prognosis. We here investigated the prognostic impact of tumor-infiltrating CD169+ macrophages in primary tumors (PTs) and their spatial relation to tumor-infiltrating B and T cells. Using two breast cancer patient cohorts, we show that CD169+ macrophages were spatially associated with the presence of B and T cell tertiary lymphoid-like structures (TLLSs) in both PTs and lymph node metastases (LNMs). While co-infiltration of CD169+/TLLS in PTs correlated with a worse prognosis, the opposite was found when present in LNMs. RNA sequencing of breast tumors further confirmed that SIGLEC1 (CD169) expression was associated with mature tertiary lymphoid structure (TLS), and Treg and Breg signatures. We propose that the negative prognostic value related to CD169+ macrophages in PTs is a consequence of an immunosuppressive tumor environment rich in TLSs, Tregs and Bregs.
|
|
| 2. |
- Kaminska, Kamila, et al.
(författare)
-
Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer
- 2021
-
Ingår i: Breast cancer research : BCR. - : Springer Science and Business Media LLC. - 1465-5411 .- 1465-542X. ; 23:1, s. 26-26
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Resistance to endocrine treatment in metastatic breast cancer is a major clinical challenge. Clinical tools to predict both drug resistance and possible treatment combination approaches to overcome it are lacking. This unmet need is mainly due to the heterogeneity underlying both the mechanisms involved in resistance development and breast cancer itself.METHODS: To study the complexity of the mechanisms involved in the resistance to the selective estrogen receptor degrader (SERD) fulvestrant, we performed comprehensive biomarker analyses using several in vitro models that recapitulate the heterogeneity of developed resistance. We further corroborated our findings in tissue samples from patients treated with fulvestrant.RESULTS: We found that different in vitro models of fulvestrant resistance show variable stability in their phenotypes, which corresponded with distinct genomic alterations. Notably, the studied models presented adaptation at different cell cycle nodes to facilitate progression through the cell cycle and responded differently to CDK inhibitors. Cyclin E2 overexpression was identified as a biomarker of a persistent fulvestrant-resistant phenotype. Comparison of pre- and post-treatment paired tumor biopsies from patients treated with fulvestrant revealed an upregulation of cyclin E2 upon development of resistance. Moreover, overexpression of this cyclin was found to be a prognostic factor determining resistance to fulvestrant and shorter progression-free survival.CONCLUSIONS: These data highlight the complexity of estrogen receptor positive breast cancer and suggest that the development of diverse resistance mechanisms dictate levels of ER independence and potentially cross-resistance to CDK inhibitors.
|
|
| 3. |
- Karlström, Jacob, et al.
(författare)
-
SRIQ clustering : A fusion of Random Forest, QT clustering, and KNN concepts
- 2022
-
Ingår i: Computational and Structural Biotechnology Journal. - : Elsevier BV. - 2001-0370. ; 20, s. 1567-1579
-
Tidskriftsartikel (refereegranskat)abstract
- Gene expression profiling together with unsupervised analysis methods, typically clustering methods, has been used extensively in cancer research to unravel, e.g., new molecular subtypes that hold promise of disease refinement that may ultimately benefit patients. However, many of the commonly used methods require a prespecified number of clusters to extract and frequently require some type of feature pre-selection, e.g. variance filtering. This introduces subjectivity to the process of cluster discovery and the definition of putative novel tumor subtypes. Here, we introduce SRIQ, a novel unsupervised clustering method that could circumvent some of the issues in commonly used unsupervised analysis methods. SRIQ incorporates concepts from random forest machine learning as well as quality threshold- and k-nearest neighbor clustering. It is implemented as a Java and Python pipeline including data pre-processing, differential expression analysis, and pathway analysis. Using 434 lung adenocarcinomas profiled by RNA sequencing, we demonstrate the technical reproducibility of SRIQ and benchmark its performance compared to the commonly used consensus clustering method. Based on differential gene expression analysis and auxiliary molecular data we show that SRIQ can define new tumor subsets that appear biologically relevant and consistent compared and that these new subgroups seem to refine existing transcriptional subtypes that were defined using consensus clustering. Together, this provides support that SRIQ may be a useful new tool for unsupervised analysis of gene expression data from human malignancies.
|
|
| 4. |
- Martin de la Fuente, Laura, et al.
(författare)
-
Detection of Copy Number Aberration and Tumor Fraction in Archival Cervical Specimens from Ovarian Cancer Patients using Shallow Whole Genome Sequencing.
- 2021
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Ovarian cancer, often called the silent killer due to its diffuse symptoms at early stage, poor prognosis after treatments and high mortality, is also a heterogeneous disease consisting of different histological subtypes with potentially different origins. About 90% of all cases derive from epithelial cells and high-grade serous ovarian carcinoma (HGSOC) is the most common and aggressive form of epithelial ovarian cancer. Recent data indicate the p53 signature lesions and serous tubal intraepithelial carcinomas (STICs) in the fallopian tube are likely to be the common origin of HGSOC, and neoplastic cells containing TP53 somatic mutations could be detected in the cervical specimens collected from 20 months to 6 years before the diagnosis. Our ongoing project is to validate pre-diagnostic cervical specimens from HGSOC by using shallow whole genome sequencing (sWGS), which can detect copy number aberrations (CNAs) even in preserved tumor DNA samples with advantages of low cost, high multiplex and easy data handling. The sWGS will be performed on Illumina sequencing platforms and the sequencing data will be processed with BWA (alignment), SAMtools (cleanup), Picardtools (duplicate) and gatk (BQSR). QDNAseq will be used for the downstream copy number analysis, and GISTIC2.0 for identifying focal gain and loss region. It will be a challenge to estimate the tumor purity and ploidy on the scarce amount of ovarian tumorigenic precursors in the cervical specimens, and we will need to use a probabilistic graphical model without a priori information from normal fallopian tissue to estimate tumor fraction, corrected CNAs as well as tumorigenic copy number signatures. We hope the sWGS approach will allow us to study and detect the early onset of ovarian cancers on large population based cervical screening in a non-invasive and cost-efficient manner.
|
|
| 5. |
- Palm, Angelica A., et al.
(författare)
-
Interferon Alpha-Inducible Protein 27 Expression Is Linked to Disease Severity in Chronic Infection of Both HIV-1 and HIV-2
- 2022
-
Ingår i: Frontiers in Virology. - : Frontiers Media SA. - 2673-818X. ; 2
-
Tidskriftsartikel (refereegranskat)abstract
- Disease progression is slower in HIV-2, as compared with HIV-1 infection, in accordance with low or undetectable plasma viremia at viral setpoint. However, it is unclear why most HIV-2 infected individuals are still at risk of developing AIDS. To explore if specific host responses are linked to HIV disease severity, we have compared blood gene expression profiles between HIV seronegative and HIV-1, HIV-2 or dually HIV-1/HIV-2 infected individuals. In this study the gene encoding Interferon alpha-inducible protein 27 (IFI27) was found to be the most differentially expressed. Detailed expression analysis revealed significantly higher IFI27 expression in HIV infected individuals compared with seronegative individuals, irrespectively of HIV type. Moreover, IFI27 expression was higher in HIV-1 than in HIV-2 infected individuals. Multiple linear regression analysis, adjusting for age and sex, showed also that plasma viral load was the strongest predictor of IFI27 expression, followed by CD4% and HIV type. In line with this, IFI27 expression was found to be higher in HIV-2 viremic, compared with HIV-2 aviremic individuals. Still, HIV-2 aviremic individuals displayed elevated IFI27 expression compared with seronegative individuals. Furthermore, in HIV-2 infected individuals, IFI27 expression was also correlated with plasma markers previously linked to inflammation and disease progression in HIV infection. Taken together, our findings suggest that sustained elevation of type I interferon signaling, here reflected by elevated IFI27 expression in the chronic infection phase, is a key pathogenic feature of both HIV-1 and HIV-2
|
|
| 6. |
- Papareddy, Praveen, et al.
(författare)
-
The role of extracellular vesicle fusion with target cells in triggering systemic inflammation
- 2024
-
Ingår i: Nature Communications. - 2041-1723. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Extracellular vesicles (EVs) play a crucial role in intercellular communication by transferring bioactive molecules from donor to recipient cells. As a result, EV fusion leads to the modulation of cellular functions and has an impact on both physiological and pathological processes in the recipient cell. This study explores the impact of EV fusion on cellular responses to inflammatory signaling. Our findings reveal that fusion renders non-responsive cells susceptible to inflammatory signaling, as evidenced by increased NF-κB activation and the release of inflammatory mediators. Syntaxin-binding protein 1 is essential for the merge and activation of intracellular signaling. Subsequent analysis show that EVs transfer their functionally active receptors to target cells, making them prone to an otherwise unresponsive state. EVs in complex with their agonist, require no further stimulation of the target cells to trigger mobilization of NF-κB. While receptor antagonists were unable to inhibit NF-κB activation, blocking of the fusion between EVs and their target cells with heparin mitigated inflammation in mice challenged with EVs.
|
|
| 7. |
- Saghir, Hani, et al.
(författare)
-
How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? A Study of Paired Core-Needle Biopsies and Surgical Specimens in Early Breast Cancer
- 2022
-
Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:16, s. 1-16
-
Tidskriftsartikel (refereegranskat)abstract
- In early breast cancer, a preoperative core-needle biopsy (CNB) is vital to confirm the malignancy of suspected lesions and for assessing the expression of treatment predictive and prognostic biomarkers in the tumor to choose the optimal treatments, emphasizing the importance of obtaining reliable results when biomarker status is assessed on a CNB specimen. This study aims to determine the concordance between biomarker status assessed as part of clinical workup on a CNB compared to a medically untreated surgical specimen. Paired CNB and surgical specimens from 259 patients that were part of the SCAN-B cohort were studied. The concordance between immunohistochemical (IHC) and gene expression (GEX) based biomarker status was investigated. Biomarkers of interest included estrogen receptor (ER; specifically, the alpha variant), progesterone receptor (PgR), Ki67, HER2, and tumor molecular subtype. In general, moderate to very good correlation in biomarker status between the paired CNB and surgical specimens was observed for both IHC assessment (83–99% agreement, kappa range 0.474–0.917) and GEX assessment (70–97% agreement, kappa range 0.552–0.800), respectively. However, using IHC, 52% of cases with low Ki67 status in the CNB shifted to high Ki67 status in the surgical specimen (McNemar’s p = 0.011). Similarly, when using GEX, a significant shift from negative to positive ER (47%) and from low to high Ki67 (16%) was observed between the CNB and surgical specimen (McNemar’s p = 0.027 and p = 0.002 respectively). When comparing biomarker status between different techniques (IHC vs. GEX) performed on either CNBs or surgical specimens, the agreement in ER, PgR, and HER2 status was generally over 80% in both CNBs and surgical specimens (kappa range 0.395–0.708), but Ki67 and tumor molecular subtype showed lower concordance levels between IHC and GEX (48–62% agreement, kappa range 0.152–0.398). These results suggest that both the techniques used for collecting tissue samples and analyzing biomarker status have the potential to affect the results of biomarker assessment, potentially also impacting treatment decisions and patient survival outcomes
|
|
| 8. |
- Veerla, Srinivas, et al.
(författare)
-
Deciphering the normal-like molecular subtype of breast cancer
- 2023
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The normal-like molecular subtype of breast cancer has not been well characterized and is currently not included in the clinically approved PAM50 molecular subtype classification. Tumors classified as normallike display high expression of basal epithelial genes and low expression of luminal epithelial genes, but also high expression of genes expressed by non-epithelial cell types including adipocytes [1]. The normal-like subtype has been suggested to represent tumors with low invasive tumor cell content, hence challenging its legitimacy as an intrinsic subtype. To clarify this issue we aimed to characterize the features of early breast cancers classified as normal-like using RNA sequencing and immunohistochemistry (IHC). Using a consecutive series of 14,000 early breast cancers from the population-based multi-center observational Sweden Cancerome Analysis Network – Breast (SCAN-B)and a recently published RNAseq-based single-sample molecular subtype predictor [2] the subtype distribution was: 39% luminal A, 25% luminal B, 12% HER2-enriched, 9% basal and 15% normal-like. The median tumor size did not differ significantly between the subtypes, while tumor cellularity assessedon H&E slides was lower among normal-like breast cancers (median 20%) compared to the other subtypes (median range 40-70%). Using a version of the classifier that excludes the normal-like subtype, i.e. akin to clinical PAM50 subtyping, 67.5% of the tumors classified as normal-like were reclassifiedas luminal A, with the remaining cases re-classified as either basal (17.5%) or HER2-enriched (14.9%). The distribution of hallmark features among normal-like tumors was 75% ER+, 67% PR+, 20% Ki67 high and 10% HER2 positive by IHC/CISH. IHC further revealed loss of E-cadherin in 30% of normal-like breast cancers, in line with 30% lobular histology. Significantly differentially expressed genes between lobular and non-lobular normal-like breast cancers included CDH1, PGC, CPB1, SERPINA6, TRH, MSLN, MMP1 and AKR1B15. The lobular normal-like breast cancers were enriched for the ER+/HER2- /node negative clinical subgroup (58%). Mutation calling using the SCAN-B MutationExplorer application [3] revealed enrichment of PIK3CA (46% vs. 18%), CDH1 (37% vs. 18%), TP53 (7% vs 0%) and ESR1 (6% vs. 0%) mutations in normal-like lobular vs. luminal lobular breast cancers. Finally, overall survival within the normal-like group was significantly different from all other subtypes and was intermediatebetween the luminal A and B groups (p<0.05 for pairwise comparisons). To conclude, the normal-like subgroup is enriched for lobular breast cancers and displays downregulation of genes involved in cell adhesion and hormone regulation. Normal-like breast cancers are primarily classified as luminal A tumorswith current clinical subtype classification algorithms, but the inferior survival and distinct features of these tumors do not preclude that this may be a true intrinsic subtype, thus warranting further investigation of the normal-like subtype.
|
|
| 9. |
- Veerla, Srinivas, et al.
(författare)
-
Kataegis in clinical and molecular subgroups of primary breast cancer
- 2024
-
Ingår i: npj Breast Cancer. - 2374-4677. ; 10:1, s. 1-13
-
Tidskriftsartikel (refereegranskat)abstract
- Kataegis is a hypermutation phenomenon characterized by localized clusters of single base pair substitution (SBS) reported in multiple cancer types. Despite a high frequency in breast cancer, large-scale analyses of kataegis patterns and associations with clinicopathological and molecular variables in established breast cancer subgroups are lacking. Therefore, WGS profiled primary breast cancers (n = 791) with associated clinical and molecular data layers, like RNA-sequencing data, were analyzed for kataegis frequency, recurrence, and associations with genomic contexts and functional elements, transcriptional patterns, driver alterations, homologous recombination deficiency (HRD), and prognosis in tumor subgroups defined by ER, PR, and HER2/ERBB2 status. Kataegis frequency was highest in the HER2-positive(p) subgroups, including both ER-negative(n)/positive(p) tumors (ERnHER2p/ERpHER2p). In TNBC, kataegis was neither associated with PAM50 nor TNBC mRNA subtypes nor with distant relapse in chemotherapy-treated patients. In ERpHER2n tumors, kataegis was associated with aggressive characteristics, including PR-negativity, molecular Luminal B subtype, higher mutational burden, higher grade, and expression of proliferation-associated genes. Recurrent kataegis loci frequently targeted regions commonly amplified in ER-positive tumors, while few recurrent loci were observed in TNBC. SBSs in kataegis loci appeared enriched in regions of open chromatin. Kataegis status was not associated with HRD in any subgroup or with distinct transcriptional patterns in unsupervised or supervised analysis. In summary, kataegis is a common hypermutation phenomenon in established breast cancer subgroups, particularly in HER2p subgroups, coinciding with an aggressive tumor phenotype in ERpHER2n disease. In TNBC, the molecular implications and associations of kataegis are less clear, including its prognostic value.
|
|
| 10. |
|
|
