Technological and computational advances driving high-throughput oncology

Engineering and computational advances have opened many new avenues in cancer research, particularly when being exploited in interdisciplinary approaches. For example, the combination of microfluidics, novel sequencing technologies, and computational analyses has been crucial to enable single-cell assays, giving a detailed picture of tumor heterogeneity for the very first time. In a similar way, these 'tech' disciplines have been elementary for generating large data sets in multidimensional cancer 'omics' approaches, cell-cell interaction screens, 3D tumor models, and tissue level analyses. In this review we summarize the most important technology and computational developments that have been or will be instrumental for transitioning classical cancer research to a large data-driven, high-throughput, high-content discipline across all biological scales.

Harmonization of PD-L1 immunohistochemistry and mRNA expression scoring in metastatic melanoma: a multicenter analysis

AIMS

This multicenter study sought to harmonize programmed death ligand 1 (PD-L1) immunohistochemistry (IHC) data and melanoma scoring. To provide a reference for PD-L1 expression independent of the IHC protocol, PD-L1 mRNA expression was determined then compared to IHC.

METHODS

Standardized PD-L1 assays (22C3, 28-8, SP142, and SP263) and laboratory-developed tests (QR1 and 22C3) were evaluated on three IHC platforms using a training set of 7 cases. mRNA expression was determined via RNAscope (CD274/PD-L1 probe) and analyzed by image analysis. PD-L1 IHC findings were scored by seven blinded pathologists using the tumor proportion score (TPS), combined positive score (CPS), and MELscore. This method was validated by three blinded pathologists on 40 metastatic melanomas.

RESULTS

Concordances among various antibody/platforms were high across antibodies (ICC > 0.80 for CPS), except for SP142. Two levels of immunostaining intensities were observed: high (QR1 and SP263) and low (28-8, 22C3, and SP142). Reproducibilities across pathologists were higher for QR1 and SP263 (ICC ≥ 0.87 and ≥ 0.85 for TPS and CPS, respectively). QR1, SP263, and 28-8 showed the highest concordance with mRNA expression (ICC ≥ 0.81 for CPS). We developed a standardized method for PD-L1 immunodetection and scoring, tested on 40 metastatic melanomas. Concordances among antibodies were excellent for all criteria, and concordances among pathologists were better for the MELscore than for other scores.

CONCLUSION

Harmonization of PD-L1 staining and scoring in melanomas with good concordance is achievable using the PD-L1 IHC protocols applied to other cancers; this reproducible approach can simplify daily practice.

Titration of apparent in-cellula affinities of protein-protein interactions

A genetic assay permits simultaneous quantification of two interacting proteins and their bound fraction at the single-cell level using flow cytometry. Apparent in-cellula affinities of protein-protein interactions can be extracted from the acquired data through a titration-like analysis. The applicability of this approach is demonstrated on a diverse set of interactions with proteins from different families and organisms and with in-vitro dissociation constants ranging from picomolar to micromolar.

Clinicopathologic analysis of trichoblastoma and comparison with nodular basal cell carcinoma

BACKGROUND

Trichoblastoma (TB) is an uncommon benign follicular tumour for which clinical data is limited since most reports originate from pathology studies.

OBJECTIVE

To describe the clinical aspects of TB.

METHODS

This is an ancillary study of a prospective multicentre cohort of 2710 clinically suspected basal cell carcinoma (BCC), including 935 nodular BCCs. Sixty-two cases were TB: they were analysed and compared to 935 nodular BCCs.

RESULTS

TB mostly occurred in females (61% vs. 43% for BCC, P<0.01) of mean age 63 years. They were located on the head and neck, mainly on the nose and forehead, in 87% of cases. The mean size was 8.1mm, 77% were<10mm (55% of BCCs, P<0.001), 8% were ulcerated (vs. 21% of BCCs, P<0.02), and 47% persisted for more than 1 year (34% of BCCs, P<0.05). Most cases had a clinical presentation similar to nodular BCC, except for 5 small, flat, white papules and 1 anfractuous plaque.

LIMITATIONS

Cases originated from a series of tumours clinically suspected as BCCs.

DISCUSSION

Some 2.6% of tumours clinically diagnosed as BCC are in fact TB. TB occurs on the head, are more frequent in women, and are smaller and of longer duration than BCC. In most cases, clinical diagnosis on clinical grounds is difficult.

Lymphomatoid papulosis types D and E: a multicentre series of the French Cutaneous Lymphomas Study Group

BACKGROUND

Lymphomatoid papulosis (LyP) type D (LyP D) and type E (LyP E) have recently been described in small series of cases or isolated case reports.

AIM

To further describe the clinical and histological features of LyP D and E based on a retrospective multicentre study.

METHODS

The clinical and histopathological features of 29 patients with an initial diagnosis of LyP D or LyP E were retrospectively assessed using standardized forms.

RESULTS

After exclusion of 5 cases, 24 patients (14 LyP D, 10 LyP E) were enrolled in the study. The median follow-up was 2.5 years (range 1 month to 13 years). LyP D was characterized by multiple recurrent self-regressing small papules that developed central erosion or necrosis, whereas LyP E presented as papulonodular lesions that rapidly evolved into necrotic eschar-like lesions > 10 mm in size. Epidermal changes were more frequent in LyP D, whereas dermal infiltrates were deeper in LyP E. Anaplastic cytology was rare and the DUSP22 rearrangement was never observed. Two patients (8%) had an associated cutaneous lymphoma.

CONCLUSION

LyP D and E have distinct clinical findings and may be associated with other cutaneous lymphomas.

Epidemiological changes in cutaneous lymphomas: an analysis of 8593 patients from the French Cutaneous Lymphoma Registry

BACKGROUND

Primary cutaneous lymphomas (PCLs) are a heterogeneous group of T-cell (CTCL) and B-cell (CBCL) malignancies. Little is known about their epidemiology at initial presentation in Europe and about potential changes over time.

OBJECTIVES

The aim of this retrospective study was to analyse the frequency of PCLs in the French Cutaneous Lymphoma Registry (GFELC) and to describe the demography of patients.

METHODS

Patients with a centrally validated diagnosis of primary PCL, diagnosed between 2005 and 2019, were included.

RESULTS

The calculated incidence was unprecedently high at 1·06 per 100 000 person-years. The number of included patients increased yearly. Most PCL subtypes were more frequent in male patients, diagnosed at a median age of 60 years. The relative frequency of rare CTCL remained stable, the proportion of classical mycosis fungoides (MF) decreased, and the frequency of its variants (e.g. folliculotropic MF) increased. Similar patterns were observed for CBCL; for example, the proportion of marginal-zone CBCL increased over time.

CONCLUSIONS

Changes in PCL frequencies may be explained by the emergence of new diagnostic criteria and better description of the entities in the most recent PCL classification. Moreover, we propose that an algorithm should be developed to confirm the diagnosis of PCL by central validation of the cases.

Gradient in cytoplasmic pressure in germline cells controls overlying epithelial cell morphogenesis

It is unknown how growth in one tissue impacts morphogenesis in a neighboring tissue. To address this, we used the Drosophila ovarian follicle, in which a cluster of 15 nurse cells and a posteriorly located oocyte are surrounded by a layer of epithelial cells. It is known that as the nurse cells grow, the overlying epithelial cells flatten in a wave that begins in the anterior. Here, we demonstrate that an anterior to posterior gradient of decreasing cytoplasmic pressure is present across the nurse cells and that this gradient acts through TGFβ to control both the triggering and the progression of the wave of epithelial cell flattening. Our data indicate that intrinsic nurse cell growth is important to control proper nurse cell pressure. Finally, we reveal that nurse cell pressure and subsequent TGFβ activity in the stretched cells combine to increase follicle elongation in the anterior, which is crucial for allowing nurse cell growth and pressure control. More generally, our results reveal that during development, inner cytoplasmic pressure in individual cells has an important role in shaping their neighbors.

A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities

We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pm to 17 μm After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.

[Reached multifocal secondary syphilis: A case presentation]

INTRODUCTION

Syphilis is a sexually transmitted infection (STI) related to Treponema pallidum. Secondary syphilis is the blood-borne systemic spread of Treponema.

OBSERVATION

We report the case of secondary syphilis in a patient without risk of STIs factor. The clinical picture began with a genital affection followed by oral erosions and ulcers and an anterior and then posterior uveitis. Serology established the diagnosis and intravenous penicillin G treatment allowed for healing.

DISCUSSION

Called the "great pretender" because of its clinical polymorphism, secondary syphilis can lead to formidable neurological and ophthalmological complications. Serological diagnosis is based on the use of treponemal and a nontreponemal tests. Penicillin G remains the treatment of choice and must be adapted according to the clinical damage.

[Primary localized cutaneous nodular amyloidosis: A diagnostic and therapeutic challenge]

BACKGROUND

Nodular primary localized cutaneous amyloidosis (PLCA) is a rare subtype of localized cutaneous amyloidosis in which amyloid protein is derived from immunoglobulin light chains. Follow-up for progression to systemic amyloidosis or autoimmune disease is mandatory. No consensus exists regarding treatment.

PATIENTS AND METHODS

We report a case of nodular PLCA in a 49-year-old man, presenting as an asymptomatic nodule of the nose. Skin biopsy revealed diffuse deposition of amyloid associated with plasmocyte proliferation. Monotypic kappa light-chain restriction was observed. Extensive systemic evaluation, including bone marrow biopsy and PET scan, was negative. Protein electrophoresis and immunofixation in serum and urine were normal. The nodule was treated with radiotherapy but there was no response. Mohs micrographic surgery (MMS) was performed with no recurrence at 6 months of follow-up. No systemic progression was observed one year after the initial diagnosis.

DISCUSSION

Since nodular PLCA may have a cutaneous presentation similar to that of primary systemic amyloidosis, evaluation for systemic amyloidosis is necessary. Treatment of amyloidosis is difficult. Radiotherapy appears ineffective in treating this type of primary cutaneous amyloidosis, and surgical treatment, where possible, is a good option, especially with MMS, which allows both controlled excision and minimal margins.

Inflammasome activation and vitiligo/nonsegmental vitiligo progression

BACKGROUND

Polymorphisms of NLR (nucleotide-binding domain and leucine rich repeat containing) family, pyrin domain containing protein 1 (NLRP1) have been found in patients with vitiligo/nonsegmental vitiligo (NSV), and increased NLRP1 expression has been detected in the leading edge of lesional skin biopsies.

OBJECTIVES

To evaluate the presence and intensity of NLRP1 immunostaining in lesional and perilesional skin of patients with vitiligo/NSV and to search for possible correlations between NLRP1 and interleukin (IL)-1β expression, lymphocytic infiltrates and disease activity.

METHODS

Of 14 consecutive vitiligo/NSV patients, eight had active disease [Vitiligo European Task Force (VETF) spreading score +1 to +5], one patient had stable disease and five patients had regressive disease (VETF spreading score -1 to -3). We performed immunostaining for NLRP1, B and T lymphocytes, IL-1β and kallikrein 7 on lesional and perilesional vitiligo skin.

RESULTS

NLRP1 and IL-1β immunostaining in perilesional vitiligo/NSV skin was significantly associated with progressive disease (P = 0·009 and 0·04, respectively) and performed better than the simple detection of lymphocytic infiltrates.

CONCLUSIONS

Our findings suggest that markers of the NLRP1 inflammasome could be a useful test for assessing disease activity in addition to the detection of inflammatory infiltrates in the progressing margins of vitiligo/NSV lesions.

[Two cases of proliferation of monoclonal and monotypic lymphocytes and plasma cells corresponding to acrodermatitis chronica atrophicans]

BACKGROUND

While a dermal proliferation of monotypic monoclonal lymphocytes and plasma cells suggests above all cutaneous marginal zone lymphoma (CMZL) or plasmacytoma, it may also correspond to a Borrelia infection of which the clinic picture is evocative, as demonstrated in the cases presented herein.

PATIENTS AND METHODS

The files of two patients were submitted for discussion at the regional multidisciplinary staff meeting on cutaneous lymphomas after review of the skin biopsies led to a diagnosis of plasmacytoma and CMZL on the basis of infiltrate containing abundant plasma cells. The infiltrates of both patients showed a kappa monotypic light chain and cutaneous B-cell clones were detected. However, the clinical features, with monomelic maculopapular rash, were evocative primarily of Borrelia infection. Diagnosis was confirmed by positive serology and clinical cure was achieved after 3 weeks of oral tetracycline, without relapse.

COMMENTS

A link between Borrelia infection and cutaneous lymphomas has long been thought to exist. Further, it is recommended that antibiotics be considered in CMZL before undertaking systemic therapy. The classic histological appearance of the tertiary phase of early-stage Lyme's disease shows perivascular and periadnexal infiltrate comprising lymphocytes and plasma cells. At the later stages, epidermal atrophy occurs with thinning of the dermis. The monoclonal and monotypic nature of skin proliferation points above all to CMZL or plasmacytoma. However, clinicopathological correlation is an essential step before such a diagnosis may be made. In the event of monomelic erythema, as in our patients, it is important to screen for Borrelia infection, which responds well to appropriate treatment.